ORCID Profile
0000-0003-2994-637X
Current Organisations
University of Oxford
,
James Cook University
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Fisheries Sciences | Population, Ecological and Evolutionary Genetics | Fish Physiology and Genetics | Aquatic Ecosystem Studies and Stock Assessment | Aquaculture | Immunology not elsewhere classified | Palaeoclimatology | Wildlife and Habitat Management | Aquaculture | Ecological Applications | Physical Geography and Environmental Geoscience | Genetics | Glaciology | Climate Change Processes | Global Change Biology | Gene Expression (incl. Microarray and other genome-wide approaches) | Other Biological Sciences | Fish Pests and Diseases | Environmental Management | Invasive Species Ecology | Fisheries Management | Gene expression (incl. microarray and other genome-wide approaches)
ANZSRC Socio-Economic Objective (SEO)
Effects of Climate Change and Variability on Antarctic and Sub-Antarctic Environments (excl. Social Impacts) | Antarctic and Sub-Antarctic Flora, Fauna and Biodiversity | Control of Animal Pests, Diseases and Exotic Species in Forest and Woodlands Environments | Wild Caught Prawns | Climate Change Adaptation Measures | Aquaculture Prawns | Ecosystem Assessment and Management of Antarctic and Sub-Antarctic Environments | Wild Caught Rock Lobster | Aquaculture Molluscs (excl. Oysters) | Aquaculture Fin Fish (excl. Tuna) | Antarctic and Sub-Antarctic Oceanography | Control of Pests, Diseases and Exotic Species not elsewhere classified | Environmental Policy, Legislation and Standards not elsewhere classified | Fisheries - Aquaculture not elsewhere classified |
Related Links
Publications
The Southern Ocean: Source and sink?
Publisher: Elsevier BV
Date: 2011
Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses
Publisher: Public Library of Science (PLoS)
Date: 25-06-2014
Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss
Publisher: Oxford University Press (OUP)
Date: 11-2020
DOI: 10.1093/GIGASCIENCE/GIAA120
Abstract: Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This erse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland. To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non–tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a erse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source. We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.
Cryptic speciation and the circumpolarity debate: A case study on endemic Southern Ocean octopuses using the COI barcode of life
Publisher: Elsevier BV
Date: 2011
DNA barcoding and molecular systematics of the benthic and demersal organisms of the CEAMARC survey
Publisher: Elsevier BV
Date: 08-2011
Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from three mitochondrial and six nuclear loci: a comparison of alignment, implied alignment and analysis methods
Publisher: Oxford University Press (OUP)
Date: 11-2007
Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2020
DOI: 10.1101/2020.02.25.951905
Abstract: Climate change at the Pleistocene/Holocene boundary reshaped many coastal landscapes, and provides an opportunity to study recent adaptive processes in marine species and ecosystems including coral reefs. On the Great Barrier Reef (GBR) sea level rise flooded a vast shelf creating a distinct inshore region which now harbours extensive coral assemblages despite being subject to relatively high turbidity, freshwater input and thermal fluctuations. To investigate how the coral holobiont has adapted to these conditions we first generated a highly contiguous genome assembly for Acropora tenuis based on long-read sequencing, and then used shallow whole-genome resequencing of 148 Acropora tenuis colonies from five inshore locations to model demographic history, identify signatures of selection and profile symbiont communities. We show that corals from Magnetic Island, located in the central inshore region of the GBR, are genetically distinct from those 50-500km further north, reflecting a Pleistocene (250-600Kya) split, whereas photosymbiont genotypes differ between reefs in a pattern more likely to reflect contemporary (Holocene) conditions. We also identified loci in the coral host genome with signatures of positive selection in the northern population and used coalescent simulations to show that these are unlikely to be accounted for by demographic history. Genes at these loci have roles in a erse range of processes that includes heterotrophic nutrition, osmotic regulation, skeletal development and the establishment and maintenance of symbiosis. Our results show that, in the case of A. tenuis holobionts from the inshore GBR, the genomes of both the coral host and the primary photosymbiont of have been significantly shaped by their environment and illustrate the complexity of adaptations that have occurred in response to past climate change.
Mitochondrial genome diversity and population structure of the giant squid Architeuthis : genetics sheds new light on one of the most enigmatic marine species
Publisher: The Royal Society
Date: 22-05-2013
Abstract: Despite its charismatic appeal to both scientists and the general public, remarkably little is known about the giant squid Architeuthis , one of the largest of the invertebrates. Although specimens of Architeuthis are becoming more readily available owing to the advancement of deep-sea fishing techniques, considerable controversy exists with regard to topics as varied as their taxonomy, biology and even behaviour. In this study, we have characterized the mitochondrial genome (mitogenome) ersity of 43 Architeuthis s les collected from across the range of the species, in order to use genetic information to provide new and otherwise difficult to obtain insights into the life of this animal. The results show no detectable phylogenetic structure at the mitochondrial level and, furthermore, that the level of nucleotide ersity is exceptionally low. These observations are consistent with the hypotheses that there is only one global species of giant squid, Architeuthis dux (Steenstrup, 1857), and that it is highly vagile, possibly dispersing through both a drifting paralarval stage and migration of larger in iduals. Demographic history analyses of the genetic data suggest that there has been a recent population expansion or selective sweep, which may explain the low level of genetic ersity.
Cross-disciplinarity in the advance of Antarctic ecosystem research
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.MARGEN.2017.09.006
Abstract: The bio ersity, ecosystem services and climate variability of the Antarctic continent and the Southern Ocean are major components of the whole Earth system. Antarctic ecosystems are driven more strongly by the physical environment than many other marine and terrestrial ecosystems. As a consequence, to understand ecological functioning, cross-disciplinary studies are especially important in Antarctic research. The conceptual study presented here is based on a workshop initiated by the Research Programme Antarctic Thresholds - Ecosystem Resilience and Adaptation of the Scientific Committee on Antarctic Research, which focussed on challenges in identifying and applying cross-disciplinary approaches in the Antarctic. Novel ideas and first steps in their implementation were clustered into eight themes. These ranged from scale problems, through risk maps, and organism/ecosystem responses to multiple environmental changes and evolutionary processes. Scaling models and data across different spatial and temporal scales were identified as an overarching challenge. Approaches to bridge gaps in Antarctic research programmes included multi-disciplinary monitoring, linking biomolecular findings and simulated physical environments, as well as integrative ecological modelling. The results of advanced cross-disciplinary approaches can contribute significantly to our knowledge of Antarctic and global ecosystem functioning, the consequences of climate change, and to global assessments that ultimately benefit humankind.
Persistent genetic signatures of historic climatic events in an Antarctic octopus
Publisher: Wiley
Date: 12-04-2012
The effect of commercial, natural and grape seed extract supplemented diets on gene expression signatures and survival of greenlip abalone (Haliotis laevigata) during heat stress
Publisher: Elsevier BV
Date: 10-2017
Microsatellite loci from the endemic Southern Ocean octopus Adelieledone polymorpha (Robson, 1930)
Publisher: Wiley
Date: 20-04-2009
DOI: 10.1111/J.1755-0998.2009.02580.X
Abstract: To determine the pattern of spatial genetic structure in the endemic Southern Ocean octopus Adelieledone polymorpha, microsatellite loci were isolated from partial genomic libraries enriched for repetitive DNA motifs. Seven dinucleotide and two trinucleotide microsatellite loci were isolated successfully and levels of polymorphism were quantified in 34 in iduals s led from the Southern Ocean near South Georgia. No pairs of microsatellite loci were linked significantly however, one locus deviated (P < 0.05) from Hardy-Weinberg equilibrium. Overall, the nine loci produced between five and 16 alleles, with observed and expected heterozygosities varying between 0.22 and 0.86 and between 0.21 and 0.94 respectively. This is the first description of microsatellite loci from an octopus endemic to the Southern Ocean, and these genetic markers are being used to quantify spatial structure within A. polymorpha.
Genomic insights of evolutionary divergence and life history innovations in Antarctic brittle stars
Publisher: Wiley
Date: 13-04-2023
DOI: 10.1111/MEC.16951
Abstract: Understanding the drivers of evolutionary innovation provides a crucial perspective of how evolutionary processes unfold across taxa and ecological systems. It has been hypothesised that the Southern Ocean provided ecological opportunities for novelty in the past. However, the drivers of innovation are challenging to pinpoint as the evolutionary genetics of Southern Ocean fauna are influenced by Quaternary glacial–interglacial cycles, oceanic currents and species ecology. Here we examined the genome‐wide single nucleotide polymorphisms of the Southern Ocean brittle stars Ophionotus victoriae (five arms, broadcaster) and O. hexactis (six arms, brooder). We found that O. victoriae and O. hexactis are closely‐related species with interspecific gene flow. During the late Pleistocene, O. victoriae likely persisted in a connected deep water refugium and in situ refugia on the Antarctic continental shelf and around Antarctic islands O. hexactis persisted exclusively within in situ island refugia. Within O. victoriae , contemporary gene flow linking to the Antarctic Circumpolar Current, regional gyres and other local oceanographic regimes was observed. Gene flow connecting West and East Antarctic islands near the Polar Front was also detected in O. hexactis . A strong association was detected between outlier loci and salinity in O. hexactis . Both O. victoriae and O. hexactis are associated with genome‐wide increase in alleles at intermediate‐frequencies the alleles associated with this peak appear to be species specific, and these intermediate‐frequency variants are far more excessive in O. hexactis . We hypothesise that the peak in alleles at intermediate frequencies could be related to adaptation in the recent past, linked to evolutionary innovations of increase in arm number and a switch to brooding from broadcasting, in O. hexactis .
Changes in tissue composition during larval development of the blacklip pearl oyster, Pinctada margaritifera (L.)
Publisher: Informa UK Limited
Date: 2003
DOI: 10.1071/MR02018
You Are What You Eat: A Genomic Analysis of the Gut Microbiome of Captive and Wild Octopus vulgaris Paralarvae and Their Zooplankton Prey
Publisher: Frontiers Media SA
Date: 31-05-2017
Poles Apart: The “Bipolar” Pteropod Species Limacina helicina Is Genetically Distinct Between the Arctic and Antarctic Oceans
Publisher: Public Library of Science (PLoS)
Date: 23-03-2010
Global drivers of recent diversification in a marine species complex
Publisher: Wiley
Date: 04-01-2021
DOI: 10.1111/MEC.15780
Genetic evidence extends the known distribution of Octopus insularis to the mid-Atlantic islands Ascension and St Helena
Publisher: Cambridge University Press (CUP)
Date: 02-09-2015
DOI: 10.1017/S0025315415000958
Abstract: Recent molecular studies have proved beneficial in providing taxonomic resolution within the Octopus vulgaris species complex, therefore aiding in the appropriate management of this high value global fisheries resource. This study used the mitochondrial ‘barcode of life’ gene Cytochrome Oxidase subunit I (COI) to investigate the identity of shallow-water benthic octopuses in the mid-Atlantic Ocean and their relationship to members of the Octopus vulgaris species complex. Maximum likelihood and Bayesian phylogenetic inference placed in iduals collected from two tropical islands, Ascension and St Helena, into a highly supported monophyletic clade with the North Brazilian species O. insularis (BS = 81, PP = 1), extending the known distribution of O. insularis to Ascension and St Helena Islands. Octopus vulgaris and two other member species of the O. vulgaris species complex, O. tetricus and O . cf. tetricus formed a highly supported monophyletic clade (BS = 99, PP = 1). Interspecific distances between the O. mimus group (O. mimus, O. bimaculoides, O. maya and O. insularis) and the O. vulgaris species group (O. vulgaris, O. tetricus and O . cf. tetricus) ranged from 14.7–26.0%, and an estimated date of ergence suggests these groups erged from a common ancestor between 19.0 and 40.9 million years ago.
Managing consequences of climate-driven species redistribution requires integration of ecology, conservation and social science
Publisher: Wiley
Date: 06-2018
DOI: 10.1111/BRV.12344
Abstract: Climate change is driving a pervasive global redistribution of the planet's species. Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach. Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges. We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems. Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change. Species redistributions present challenges for human well-being, environmental management and sustainable development. By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution. Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges. Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human-centred approaches. Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions.
Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework
Publisher: Elsevier BV
Date: 11-2005
DOI: 10.1016/J.YMPEV.2005.03.020
Abstract: The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and v ire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes) (3) the family Octopodidae, as currently defined, is paraphyletic (4) the superfamily Argonautoidea are basal within the suborder Incirrata and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.
The thermohaline expressway: the Southern Ocean as a centre of origin for deep‐sea octopuses
Publisher: Wiley
Date: 21-11-2008
DOI: 10.1111/J.1096-0031.2008.00234.X
Abstract: Understanding how environmental forcing has generated and maintained large-scale patterns of bio ersity is a key goal of evolutionary research and critical to predicting the impacts of global climate change. We suggest that the initiation of the global thermohaline circulation provided a mechanism for the radiation of Southern Ocean fauna into the deep sea. We test this hypothesis using a relaxed phylogenetic approach to coestimate phylogeny and ergence times for a lineage of octopuses with Antarctic and deep-sea representatives. We show that the deep-sea lineage had their evolutionary origins in Antarctica, and estimate that this lineage erged around 33 million years ago (Ma) and subsequently radiated at 15 Ma. Both of these dates are critical in development of the thermohaline circulation and we suggest that this has acted as an evolutionary driver enabling the Southern Ocean to become a centre of origin for deep-sea fauna. This is the first unequivocal molecular evidence that deep-sea fauna from other ocean basins originated from Southern Ocean taxa and this is the first evidence to be dated. © The Willi Hennig Society 2008.
Genetic diversity and population structure of the threatened freshwater catfish, Tandanus tandanus, in Victoria, Australia
Publisher: Springer Science and Business Media LLC
Date: 26-09-2014
Oceanographic processes shape genetic signatures of planktonic cephalopod paralarvae in two upwelling regions
Publisher: Elsevier BV
Date: 2019
Divergence time estimates for major cephalopod groups: evidence from multiple genes
Publisher: Wiley
Date: 31-01-2006
DOI: 10.1111/J.1096-0031.2006.00086.X
Abstract: This is the first study to use both molecular and fossil data to date the ergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary ergences within the group. Divergence time analyses were performed using the Thorne/Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders V yromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated ergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have erged in the Mesozoic, with a radiation of many taxa around the Cretaceous/Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient ersification of this group.
Disentangling genetic from environmental effects on phenotypic variability of southern rock lobster (Jasus edwardsii) postlarvae
Publisher: Wiley
Date: 11-2022
DOI: 10.1002/ECE3.9519
Abstract: Environmental conditions experienced during the larval dispersal of marine organisms can determine the size‐at‐settlement of recruits. It is, therefore, not uncommon that larvae undergoing different dispersal histories would exhibit phenotypic variability at recruitment. Here, we investigated morphological differences in recently settled southern rock lobster ( Jasus edwardsii ) recruits, known as pueruli, along a latitudinal and temporal gradient on the east coast of Tasmania, Australia. We further explored whether natural selection could be driving morphological variation. We used double digest restriction site‐associated DNA sequencing (ddRADseq) to assess differences in the genetic structure of recently settled recruits on the east coast of Tasmania over 3 months of peak settlement during 2012 (August–October). Phenotypic differences in pueruli between sites and months of settlement were observed, with significantly smaller in iduals found at the northernmost site. Also, there was a lack of overall genetic ergence however, significant differences in pairwise F ST values between settlement months were observed at the southernmost study site, located at an area of confluence of ocean currents. Specifically, in iduals settling into the southernmost earlier in the season were genetically different from those settling later. The lack of overall genetic ergence in the presence of phenotypic variation indicates that larval environmental history during the dispersal of J. edwardsii could be a possible driver of the resulting phenotype of settlers.
Toxicity in Cephalopods
Publisher: Springer Netherlands
Date: 2015
Small copepods could channel missing carbon through metazoan predation
Publisher: Wiley
Date: 30-10-2018
DOI: 10.1002/ECE3.4546
What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda?
Publisher: Oxford University Press (OUP)
Date: 12-01-2161
The macro- and megabenthic fauna on the continental shelf of the eastern Amundsen Sea, Antarctica
Publisher: Elsevier BV
Date: 10-2013
Positive selection in octopus haemocyanin indicates functional links to temperature adaptation
Publisher: Springer Science and Business Media LLC
Date: 05-07-2015
Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum
Publisher: Oxford University Press (OUP)
Date: 10-2022
Abstract: Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effect of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype-phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid ergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid ergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes, and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
A panel of microsatellite loci from two species of octopus, Pareledone turqueti (Joubin, 1905) and Pareledone charcoti (Joubin, 1905)
Publisher: Wiley
Date: 22-06-2009
DOI: 10.1111/J.1755-0998.2009.02617.X
Abstract: Eighteen dinucleotide microsatellite loci were isolated from two octopus species, Pareledone turqueti and Pareledone charcoti, which are endemic to the Southern Ocean. Genetic ersity was assessed in s les of P. charcoti and P. turqueti from Elephant Island and Shag Rocks respectively. All except one locus (which has proved to be polymorphic in other species) were variable in the focal species and lified between six and 30 and between four and 28 alleles for P. charcoti and P. turqueti respectively mean expected heterozygosities varied between 0.38 and 0.95 (P. charcoti) and between 0.34 and 0.97 (P. turqueti), with significant (P < 0.05) departures from Hardy-Weinberg equilibrium at seven loci three of these loci provided significant (P < 0.05) evidence for null alleles. Two pairs of loci isolated from P. turqueti demonstrated significant (P < 0.05) linkage disequilibrium. We are presently using these genetic markers to quantify spatial genetic structure in the genus Pareledone.
Whole mitochondrial genome of the Ram's Horn Squid shines light on the phylogenetic position of the monotypic order Spirulida (Haeckel, 1896)
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.YMPEV.2017.01.011
Abstract: The phylogenetic position of the only known species within the order Spirulida, the Ram's Horn Squid, Spirula spirula, may be the key to resolving relationships within Decapodiformes (squids and cuttlefishes). Spirula spirula possesses several unique features including an internal calcareous chambered shell unlike the familiar cuttlebone of Sepiidae (cuttlefishes). The shell is reduced to a gladius or absent in other decapod clades. To resolve decapodiform phylogenetic relationships we sequenced the mitochondrial genome of S. spirula and Sepiadarium austrinum and analysed these along with other mitochondrial genomes. Sequence analyses found that S. spirula and Sepiidae, the only two extant phragmocone bearing groups, were not sister taxa. Rather, in most analyses S. spirula was placed within a clade containing Bathyteuthoidea and Oegopsida either as the sister taxon to Bathyteuthoidea+Oegopsida or the sister taxon to Bathyteuthoidea only, depending upon the analysis method. Sepiidae was the sister taxon to a clade containing all remaining decapods. Spirulid mitochondrial gene order was identical to that of Octopodiformes, which we recognize as close to that of ancestral molluscs. The phylogenetic position of Idiosepiidae differed among analysis methods of molecular sequence data. However, gene order analysis resolved a highly supported monophyletic relationship containing Idiosepiidae and Sepiolida.
A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda)
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.JPROT.2016.07.026
Abstract: Sepiadarium austrinum, the southern bottletail squid, is a small squid that inhabits soft sediments along Australia's south-east coast. When provoked, it rapidly secretes large volumes of slime, presumably as a form of chemical defense. We analyzed the proteomic composition of this slime using tandem mass spectrometry and transcriptomics and found that it was remarkably complex with 1735 identified protein groups (FDR:0.01). To investigate the chemical defense hypothesis we performed an Artemia toxicity assay and used sequence analysis to search for toxin-like molecules. Although the slime did not appear to be toxic to Artemia we found 13 proteins in slime with the hallmarks of toxins, namely cysteine richness, short length, a signal peptide and/or homology to known toxins. These included three short (80-130AA) cysteine rich secreted proteins with no homology to proteins on the NCBI or UniProt databases. Other protein families found included, CAP, phospholipase-B, ShKT-like peptides, peptidase S10, Kunitz BPTI and DNase II. Quantitative analysis using intensity based absolute quantification (iBAQ via MaxQuant) revealed 20 highly abundant proteins, accounting for 67% of iBAQ signal, and three of these were toxin-like. No mucin homologues were found suggesting that the structure of the slime gel may be formed by an unknown mechanism. This study is the first known instance of a slime secretion from a cephalopod to be analyzed by proteomics methods and is the first investigation of a member of the family Sepiadariidae using proteomic methods. 1735 proteins were identified with 13 of these fitting criteria established for the identification of putative toxins. The slime is dominated by 20 highly abundant proteins with secreted, cysteine rich proteins. The study highlights the importance of 'omics approaches in understanding novel organisms.
Molecular evolutionary relationships of the octopodid genus Thaumeledone (Cephalopoda: Octopodidae) from the Southern Ocean
Publisher: Cambridge University Press (CUP)
Date: 19-05-2008
DOI: 10.1017/S0954102008001132
Abstract: Recent trawling in the Southern Ocean has yielded in iduals of a number of species of the deep sea octopod genus Thaumeledone. This paper provides the first molecular study of the genus, employing molecular sequences from five mitochondrial (12S rDNA, 16S rDNA, COI, COIII, cytochrome oxidase b ) and a single nuclear gene ( rhodopsin ) and includes representatives of each of the known Southern Ocean species. Thaumeledone rotunda , believed to be circumpolar in distribution and found in relatively deep water is the sister taxa to T. gunteri , known only from South Georgia. A notable level of sequence variability was evident between a T. peninsulae in idual recently captured from the Powell Basin, and two T. peninsulae in iduals captured from the continental slope, north of the South Shetland Islands. This is likely to represent population level intraspecific variation within this species.
Erratum: Positive selection in octopus haemocyanin indicates functional links to temperature adaptation (BMC Evolutionary Biology)
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Detecting glacial refugia in the Southern Ocean
Publisher: Wiley
Date: 23-03-2020
DOI: 10.1111/ECOG.04951
Using genomics and morphometrics to monitor data-poor and commercially exploited octopod populations
Publisher: Springer Science and Business Media LLC
Date: 26-08-2023
DOI: 10.1007/S00227-023-04270-9
Abstract: Over 150 species of benthic octopods have been described within the ‘catch-all’ Octopus genus (Family: Octopodidae) and yet, many Octopus species harvested by fisheries remain unidentified to species-level due to a lack of distinguishing traits. Within species, there is also limited information on how populations differ genetically and the level of connectivity between populations. Therefore, we s led octopods from commercial fisheries in southeast Australia, in order to identify the species, examine the phylogeographic relationships among species and the level of population genetic structuring within species, as well as to look for any adaptive genetic variation. The mitochondrial gene, cytochrome oxidase subunit III (COIII), was sequenced in 346 octopods along with single nucleotide polymorphisms using double digest restriction site-associated DNA sequencing (ddRADseq). Morphometric traits were also measured in mature specimens. The southern keeled octopus ( ‘Octopus’ berrima ) and pale octopus ( ‘Octopus’ pallidus ) were identified using COIII data. For ‘Octopus’ berrima , we found that some populations whilst being morphologically similar were genetically distinct. In contrast, ‘Octopus’ pallidus populations were both morphologically and genetically distinct across the studied regions. Our results provide key information to better inform conservation and management decisions for developing octopod fisheries in southeast Australia and highlight the importance of genomics tools in the conservation management of commercially and recreationally important species.
Combined Transcriptomic and Proteomic Analysis of the Posterior Salivary Gland from the Southern Blue-Ringed Octopus and the Southern Sand Octopus
Publisher: American Chemical Society (ACS)
Date: 05-08-2016
DOI: 10.1021/ACS.JPROTEOME.6B00452
Abstract: This study provides comprehensive proteomic profiles from the venom producing posterior salivary glands of octopus (superorder Octopodiformes) species. A combined transcriptomic and proteomic approach was used to identify 1703 proteins from the posterior salivary gland of the southern blue-ringed octopus, Hapalochlaena maculosa and 1300 proteins from the posterior salivary gland of the southern sand octopus, Octopus kaurna. The two proteomes were broadly similar clustering of proteins into orthogroups revealed 937 that were shared between species. Serine proteases were particularly erse and abundant in both species. Other abundant proteins included a large number of secreted proteins, many of which had no known conserved domains, or homology to proteins with known function. On the basis of homology to known venom proteins, 23 putative toxins were identified in H. maculosa and 24 in O. kaurna. These toxins span nine protein families: CAP (cysteine rich secretory proteins, antigen 5, parthenogenesis related), chitinase, carboxylesterase, DNase, hyaluronidase, metalloprotease, phospholipase, serine protease and tachykinin. Serine proteases were responsible for 70.9% and 86.3% of putative toxin expression in H. maculosa and O. kaurna, respectively, as determined using intensity based absolute quantification (iBAQ) measurements. Phylogenetic analysis of the putative toxin serine proteases revealed a similar suite of erse proteins present in both species. Posterior salivary gland composition of H. maculosa and O. kaurna differ in several key aspects. While O. kaurna expressed the proteinaceous neurotoxin, tachykinin, this was absent from H. maculosa, perhaps reflecting the acquisition of a potent nonproteinaceous neurotoxin, tetrodotoxin (TTX) produced by bacteria in the salivary glands of that species. The dispersal factor, hyaluronidase was particularly abundant in H. maculosa. Chitinase was abundant in both species and is believed to facilitate envenomation in chitinous prey such as crustaceans. Cephalopods represent a largely unexplored source of novel proteins distinct from all other venomous taxa and are of interest for further inquiry, as novel proteinaceous toxins derived from venoms may contribute to pharmaceutical design.
A coleoid gladius (Mollusca, Cephalopoda) from the Albian of Normandy (France): A new squid genus and species
Publisher: Elsevier BV
Date: 07-2013
Dating Antarctic ice sheet collapse: Proposing a molecular genetic approach
Publisher: Elsevier BV
Date: 2018
Expanded description of Opisthoteuthis hardyi based on new specimens from the Patagonian slope
Publisher: Cambridge University Press (CUP)
Date: 09-07-2009
DOI: 10.1017/S0025315409000988
Abstract: Opisthoteuthis hardyi was originally described from a single male specimen caught near Shag Rocks (north-west of South Georgia) and no further specimens have been attributed to this species. During research fishing on the Patagonian slope to the south-east of the Falkland Islands 33 specimens of Opisthoteuthis were caught at depths ranging from 630 to 1391 m. Morphological measurements indicated that these specimens were conspecific to the holotype of O. hardyi . The mitochondrial gene 16S rDNA was sequenced from two of these specimens and compared with a published sequence of the holotype and other Opisthoteuthidae to confirm the morphological data. This extends the geographical and bathymetric range of the species, which spans the Antarctic Polar Front. We also expand the original description, providing details of the digestive system and of the female reproductive system, with preliminary estimates of fecundity.
A new pygmy squid, Idiosepius hallami n. sp. (Cephalopoda: Idiosepiidae) <br />from eastern Australia and elevation of the southern endemic ‘notoides’ clade to a new genus, Xipholeptos n. gen.
Publisher: Magnolia Press
Date: 08-01-2018
DOI: 10.11646/ZOOTAXA.4369.4.1
Abstract: A new species of pygmy squid, Idiosepius hallami n. sp., is described from eastern Australia. It differs from I. notoides Berry, 1921 and I. pygmaeus Steenstrup, 1881 (also found in Australian waters) in a number of traits, including the number of club suckers, shape of the funnel-mantle locking apparatus and the modification of the male hectocotylus. Mitochondrial DNA markers (12S rRNA, 16S rRNA and cytochrome c oxidase subunit 1) indicate that it is also distinct on a molecular level. The new Australian species is also recognised as the taxon from Stradbroke I., Queensland for which the entire mitochondrial genome has been sequenced (Hall et al. 2014). Idiosepius hallami n. sp. is compared with all nominal Idiosepius Steenstrup, 1881 and a current summary of Idiosepius systematics is provided as a basis for future studies. Based on our analyses, we propose the elevation of the ‘notoides’ clade to the new genus Xipholeptos n. gen., retaining Idiosepius as the genetic epithet for all other nominal idiosepiids. This is supported by: monophyly of the two lineages based on molecular data sets, the level of sequence ergence between these lineages, and morphological differences. The ‘notoides’ clade is endemic to southern Australia and its basal phylogenetic position suggests that the family may have originated in the Australasian region. Idiosepiids are found in seagrass beds and among mangroves—among the most threatened ecosystems in the world.
Co-estimation of phylogeny and divergence times of Argonautoidea using relaxed phylogenetics
Publisher: Elsevier BV
Date: 03-2010
DOI: 10.1016/J.YMPEV.2009.11.017
Abstract: This is the first study to investigate molecular phylogenetic relationships among all four genera of the superfamily Argonautoidea, a clade of erse pelagic cephalopods with extraordinary characters such as ovoviviparity, dwarf males and secondary "shell" development. Phylogenetic relationships and ergence times within the superfamily were co-estimated using relaxed phylogenetic techniques. A sister-taxon relationship was recovered between Argonauta and Ocythoe and between Tremoctopus and Haliphron. The most recent common ancestor of Argonautoidea was estimated to date from the early Tertiary under the scenario that a lack of a "shell" in the ocythoid lineage is a primary characteristic. In contrast, a later Tertiary most recent common ancestor was estimated under the scenario that a "shell" was present in the early ocythoid lineage and was subsequently lost.
Patterns, processes and vulnerability of Southern Ocean benthos: a decadal leap in knowledge and understanding
Publisher: Springer Science and Business Media LLC
Date: 25-04-2013
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
Publisher: Oxford University Press (OUP)
Date: 19-07-2020
DOI: 10.1093/BIOINFORMATICS/BTAA653
Abstract: Antimicrobial peptides (AMPs) are the key components of the innate immune system that protect against pathogens, regulate the microbiome and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ir. ir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. ir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at egana/ ir. Supplementary data are available at Bioinformatics online.
Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata
Publisher: Springer Science and Business Media LLC
Date: 27-03-2017
The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review
Publisher: Informa UK Limited
Date: 18-02-2014
Future challenges in cephalopod research
Publisher: Cambridge University Press (CUP)
Date: 26-06-2014
DOI: 10.1017/S0025315414000782
Abstract: Cephalopods (Mollusca: Cephalopoda) play an important role as keystone invertebrates in various marine ecosystems, as well as being a valuable fisheries resource. At the World Malacological Congress, held 21–28 July 2013 in Ponta Delgada, Azores, Portugal, a number of cephalopod experts convened to honour the contribution of the late Malcolm R. Clarke, FRS (1930–2013) to cephalopod research. Endorsed by the Cephalopod International Advisory Council (CIAC), the meeting discussed some of the major challenges that cephalopod research will face in the future. These challenges were identified as follows: (1) to find new ways to ascertain the trophic role and food web links of cephalopods using hard tissues, stable isotopes and novel concepts in theoretical ecology (2) to explore new approaches to the study of cephalopod morphology (3) to further develop cephalopod aquaculture research (4) to find new ways to ascertain cephalopod adaptation and response to environmental change (5) to strengthen cephalopod genetics research and (6) to develop new approaches for cephalopod fisheries and conservation. The present paper presents brief reviews on these topics, followed by a discussion of the general challenges that cephalopod research is bound to face in the near future. By contributing to initiatives both within CIAC and independent of CIAC, the principle aim of the paper is to stimulate future cephalopod research.
Widespread hybridization in the introduced hog deer population of Victoria, Australia, and its implications for conservation
Publisher: Wiley
Date: 09-2019
DOI: 10.1002/ECE3.5603
Amundsen Sea Mollusca from the BIOPEARL II expedition
Publisher: Pensoft Publishers
Date: 22-04-2013
A new species of Pareledone (Cephalopoda: Octopodidae) from Antarctic Peninsula Waters
Publisher: Springer Science and Business Media LLC
Date: 16-01-2007
Evolutionary innovations in Antarctic brittle stars linked to glacial refugia
Publisher: Wiley
Date: 29-11-2021
DOI: 10.1002/ECE3.8376
Abstract: The drivers behind evolutionary innovations such as contrasting life histories and morphological change are central questions of evolutionary biology. However, the environmental and ecological contexts linked to evolutionary innovations are generally unclear. During the Pleistocene glacial cycles, grounded ice sheets expanded across the Southern Ocean continental shelf. Limited ice‐free areas remained, and fauna were isolated from other refugial populations. Survival in Southern Ocean refugia could present opportunities for ecological adaptation and evolutionary innovation. Here, we reconstructed the phylogeographic patterns of circum‐Antarctic brittle stars Ophionotus victoriae and O . hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). We examined the evolutionary relationship between the two species using cytochrome c oxidase subunit I (COI) data. COI data suggested that O . victoriae is a single species (rather than a species complex) and is closely related to O . hexactis (a separate species). Since their recent ergence in the mid‐Pleistocene, O . victoriae and O . hexactis likely persisted differently throughout glacial maxima, in deep‐sea and Antarctic island refugia, respectively. Genetic connectivity, within and between the Antarctic continental shelf and islands, was also observed and could be linked to the Antarctic Circumpolar Current and local oceanographic regimes. Signatures of a probable seascape corridor linking connectivity between the Scotia Sea and Prydz Bay are also highlighted. We suggest that survival in Antarctic island refugia was associated with increase in arm number and a switch from broadcast spawning to brooding in O . hexactis , and propose that it could be linked to environmental changes (such as salinity) associated with intensified interglacial‐glacial cycles.
Body Size, Growth and Life Span: Implications for the Polewards Range Shift of Octopus tetricus in South-Eastern Australia
Publisher: Public Library of Science (PLoS)
Date: 04-08-2014
Emerging biological archives can reveal ecological and climatic change in Antarctica
Publisher: Wiley
Date: 08-09-2022
DOI: 10.1111/GCB.16356
Abstract: Anthropogenic climate change is causing observable changes in Antarctica and the Southern Ocean including increased air and ocean temperatures, glacial melt leading to sea‐level rise and a reduction in salinity, and changes to freshwater water availability on land. These changes impact local Antarctic ecosystems and the Earth's climate system. The Antarctic has experienced significant past environmental change, including cycles of glaciation over the Quaternary Period (the past ~2.6 million years). Understanding Antarctica's paleoecosystems, and the corresponding paleoenvironments and climates that have shaped them, provides insight into present day ecosystem change, and importantly, helps constrain model projections of future change. Biological archives such as extant moss beds and peat profiles, biological proxies in lake and marine sediments, vertebrate animal colonies, and extant terrestrial and benthic marine invertebrates, complement other Antarctic paleoclimate archives by recording the nature and rate of past ecological change, the paleoenvironmental drivers of that change, and constrain current ecosystem and climate models. These archives provide invaluable information about terrestrial ice‐free areas, a key location for Antarctic bio ersity, and the continental margin which is important for understanding ice sheet dynamics. Recent significant advances in analytical techniques (e.g., genomics, biogeochemical analyses) have led to new applications and greater power in elucidating the environmental records contained within biological archives. Paleoecological and paleoclimate discoveries derived from biological archives, and integration with existing data from other paleoclimate data sources, will significantly expand our understanding of past, present, and future ecological change, alongside climate change, in a unique, globally significant region.
Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas
Publisher: PeerJ
Date: 12-02-2018
DOI: 10.7717/PEERJ.4331
Abstract: Comprising more than 800 extant species, the class Cephalopoda (octopuses, squid, cuttlefish, and nautiluses) is a fascinating group of marine conchiferan mollusks. Recently, the first cephalopod genome (of Octopus bimaculoides ) was published, providing a genomic framework, which will enable more detailed investigations of cephalopod characteristics, including developmental, morphological, and behavioural traits. Meanwhile, a robust phylogeny of the members of the subclass Coleoidea (octopuses, squid, cuttlefishes) is crucial for comparative and evolutionary studies aiming to investigate the group’s traits and innovations, but such a phylogeny has proven very challenging to obtain. Here, we present the results of phylogenetic inference at the genus level using mitochondrial and nuclear marker sequences available from public databases. Topologies are presented which show support for (1) the monophyly of the two main superorders, Octobrachia and Decabrachia, and (2) some of the interrelationships at the family level. We have mapped morphological characters onto the tree and conducted molecular dating analyses, obtaining congruent results with previous estimates of ergence in major lineages. Our study also identifies unresolved phylogenetic relationships within the cephalopod phylogeny and insufficient taxonomic s ling among squids excluding the Loliginidae in the Decabrachia and within the Order Cirromorphida in the Octobrachia. Genomic and transcriptomic resources should enable resolution of these issues in the relatively near future. We provide our alignment as an open access resource, to allow other researchers to reconstruct phylogenetic trees upon this work in the future.
Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 31-03-2017
Abstract: Distributions of Earth's species are changing at accelerating rates, increasingly driven by human-mediated climate change. Such changes are already altering the composition of ecological communities, but beyond conservation of natural systems, how and why does this matter? We review evidence that climate-driven species redistribution at regional to global scales affects ecosystem functioning, human well-being, and the dynamics of climate change itself. Production of natural resources required for food security, patterns of disease transmission, and processes of carbon sequestration are all altered by changes in species distribution. Consideration of these effects of bio ersity redistribution is critical yet lacking in most mitigation and adaptation strategies, including the United Nation's Sustainable Development Goals.
Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum
Publisher: Cold Spring Harbor Laboratory
Date: 05-04-2022
DOI: 10.1101/2022.04.02.486852
Abstract: Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera . We show that three genetically distinct populations are present in northwestern Australia, and that their rapid ergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid ergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi
Publisher: Springer Science and Business Media LLC
Date: 15-11-2018
Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non‐environmental DNA specialists
Publisher: Wiley
Date: 28-03-2020
DOI: 10.1111/ACV.12583
The ink sac clouds octopod evolutionary history
Publisher: Springer Science and Business Media LLC
Date: 28-05-2013
A mitochondrial phylogeny of the family Onychoteuthidae (Cephalopoda: Oegopsida)
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.YMPEV.2018.05.032
Abstract: The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 in iduals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia) 29 genetically distinct species were recovered, with the BIN (Barcode Index Number) analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family ersity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the ersity and evolutionary relationships for the Onychoteuthidae can be achieved.
The complete mitochondrial genome of the pygmy squid,Idiosepius(Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae
Publisher: Informa UK Limited
Date: 17-01-2014
DOI: 10.3109/19401736.2013.865180
Abstract: We report the first complete mitochondrial genome of the pygmy squid, Idiosepius, (Idiosepiidae). The mtDNA genome is 16,183 bp long with an AT content of 75.4%. All conserved metazoan mitochondrial genes are identified with the addition of a 1018 bp non-coding region. Idiosepius gene order most closely resembles that of the bobtail squid Semirossia (Sepiolidae).
Cephalopod genomics: A plan of strategies and organization
Publisher: Springer Science and Business Media LLC
Date: 26-09-2012
DOI: 10.4056/SIGS.3136559
Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial Period
Publisher: Cold Spring Harbor Laboratory
Date: 31-01-2023
DOI: 10.1101/2023.01.29.525778
Abstract: The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to collapse under future climate trajectories and may even lie within the mitigated warming scenarios of 1.5–2 °C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates, including the Last Interglacial period, when global sea levels were 5–10 m higher than today, and global average temperatures of 0.5–1.5 °C warmer, could resolve this uncertainty. Here we show, using a panel of genome-wide, single nucleotide polymorphisms of a circum-Antarctic octopus, persistent, historic signals of gene flow only possible with complete WAIS collapse. Our results provide the first empirical evidence that the tipping point of WAIS loss could be reached even under stringent climate mitigation scenarios. Historical gene flow in marine animals indicate the West Antarctic ice sheet collapsed during the Last Interglacial period.
How useful are the recommended counts and indices in the systematics of the Octopodidae (Mollusca: Cephalopoda)
Publisher: Oxford University Press (OUP)
Date: 24-09-2008
Profiles: Kudos for female Antarctic researchers
Publisher: Springer Science and Business Media LLC
Date: 08-2016
DOI: 10.1038/536148B
Cranchiids of the South Atlantic Mid-Oceanic Ridge: results from the first southern MAR-ECO expedition
Publisher: Informa UK Limited
Date: 24-02-2014
Southern Ocean Evolution in a Global Context: A Molecular Viewpoint
Publisher: Springer Berlin Heidelberg
Date: 30-10-2012
A snail's pace: A preliminary analysis of the effects of stress and genetics on movement of Haliotis
Publisher: Elsevier BV
Date: 02-2013
A redescription of the fossil coleoid cephalopod genusPalaeololigoNaef, 1921 (Decapodiformes: Palaeololiginidae) and its relationship to Recent squids
Publisher: Informa UK Limited
Date: 24-05-2010
Global drivers of diversification in a marine species complex
Publisher: Cold Spring Harbor Laboratory
Date: 15-12-2019
DOI: 10.1101/2019.12.13.874883
Abstract: Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome ergence before speciation. The processes influencing species ersification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide ergence, introgression patterns and inferred demographic history between species pairs of all extant rock lobster species ( Jasus spp.), a complex with long larval duration, that has populated continental shelf and seamount habitats around the globe at approximately 40°S. Genetic differentiation patterns revealed the effects of the environment and geographic isolation. Species associated with the same habitat structure (either continental shelf or seamount/island) shared a common ancestry, even though the habitats were not adjacent. Differences in benthic temperature explained a significant proportion (41.3%) of the genetic differentiation. The Eastern Pacific species pair of J. caveorum and J. frontalis retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa and seamounts in the Indian and Atlantic oceans included events of introgression after secondary contact. Parameters estimated for time in isolation and gene flow were congruent with genetic differentiation metrics suggesting that the observed differentiation patterns are the product of migration and genetic drift. Our results reveal important effects of habitat and demographic processes on the ergence of species within the genus Jasus providing the first empirical study of genome-wide drivers of ersification that incorporates all extant species in a marine genus with long pelagic larval duration.
Is the Southern Ocean ecosystem primed for change or at the cliff edge?
Publisher: Wiley
Date: 23-05-2022
DOI: 10.1111/GCB.16224
Abstract: The Southern Ocean is experiencing unprecedented environmental risks and consequences from current climate change. It is unclear how the benthic fauna, which has largely evolved in isolation, will respond to future changes. Knowing how the benthic fauna persisted through repeated extreme glacial-interglacial cycles in the past provides a unique opportunity to inform future predictions. Right now, understanding and preserving current genetic ersity and connectivity between populations will give species the best chance to adapt.
De Novo Characterisation of the Greenlip Abalone Transcriptome (Haliotis laevigata) with a Focus on the Heat Shock Protein 70 (HSP70) Family
Publisher: Springer Science and Business Media LLC
Date: 31-07-2014
DOI: 10.1007/S10126-014-9591-Y
Abstract: Abalone (Haliotis) are economically important molluscs for fisheries and aquaculture industries worldwide. Despite this, genomic resources for abalone and molluscs are still limited. Here we present a description and functional annotation of the greenlip abalone (Haliotis laevigata) transcriptome. We present a focused analysis on the heat shock protein 70 (HSP70) family of genes with putative functions affecting temperature stress and immunity. A total of ~38 million paired end Illumina reads were obtained, resulting in a Trinity assembly of 222,172 contigs with minimum length of 200 base pairs and maximum length of 33 kilobases. The 20,702 contigs were annotated with gene descriptions by BLAST. We created a program to maximise the number of functionally annotated genes, and over 10,000 contigs were assigned Gene ontologies (GO terms). By using CateGOrizer, immunity related GO terms for stressors such as heat, hypoxia, oxidative stress and wounding received the highest counts. Twenty-six contigs with homology to the HSP70 family of genes were identified. Ninety-one putative single-nucleotide polymorphisms were observed in the abalone HSP70 contigs. Eleven of these were considered non-synonymous. The annotated transcriptome described in this study will be a useful basis for future work investigating the genetic response of abalone to stress.
Low-coverage MiSeq next generation sequencing reveals the mitochondrial genome of the Eastern Rock Lobster,Sagmariasus verreauxi
Publisher: Informa UK Limited
Date: 10-01-2014
DOI: 10.3109/19401736.2013.855921
Abstract: The complete mitochondrial genome of the Eastern Rock lobster, Sagmariasus verreauxi, is reported for the first time. Using low-coverage, long read MiSeq next generation sequencing, we constructed and determined the mtDNA genome organization of the 15,470 bp sequence from two isolates from Eastern Tasmania, Australia and Northern New Zealand, and identified 46 polymorphic nucleotides between the two sequences. This genome sequence and its genetic polymorphisms will likely be useful in understanding the distribution and population connectivity of the Eastern Rock Lobster, and in the fisheries management of this commercially important species.
Can environmental DNA be used to detect first arrivals of the cane toad, Rhinella marina, into novel locations?
Publisher: Wiley
Date: 27-06-2020
DOI: 10.1002/EDN3.114
Investigation of Genetic Structure between Deep and Shallow Populations of the Southern Rock Lobster, Jasus edwardsii in Tasmania, Australia
Publisher: Public Library of Science (PLoS)
Date: 18-10-2013
Reproductive capacity of a marine species (Octopus tetricus) within a recent range extension area
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/MF14126
Abstract: To persist in the face of environmental change, species must adjust to the new conditions or change their geographical distribution, e.g. by range extension. Success for in iduals within a zone of range extension requires the new environment to support their capacity to produce viable gametes and survival of the offspring. Reproductive characteristics of the polewards range-shifting Octopus tetricus were examined within the new range off north-eastern Tasmania, Australia, to assess whether it is likely to successfully establish in this extended area of its range. Approximately 44% of captured males and 14% of captured females were mature. Mature females with developing eggs were found throughout the year. Greater numbers of mature females were observed during the austral summer and spring, whereas mature males were observed all year round. Fecundity was high and developing embryos appeared to be viable. Our results suggest that O. tetricus is successfully reproducing beyond its historical range, the reproductive cycle is timed to favourable environmental conditions, and the population has the potential to be self-sustainable. The reproductive biology of O. tetricus may thus facilitate the establishment and prevalence of the population into new environments beyond the known historical distribution.
The complete mitochondrial genome of Axis porcinus (Mammalia: Cervidae) from Victoria, Australia, using MiSeq sequencing
Publisher: Informa UK Limited
Date: 26-07-2017
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
Publisher: Cold Spring Harbor Laboratory
Date: 08-05-2020
DOI: 10.1101/2020.05.07.082412
Abstract: Antimicrobial peptides (AMPs) are key components of the innate immune system that protect against pathogens, regulate the microbiome, and are promising targets for pharmaceutical research. Computational tools based on machine learning have the potential to aid discovery of genes encoding novel AMPs but existing approaches are not designed for genome-wide scans. To facilitate such genome-wide discovery of AMPs we developed a fast and accurate AMP classification framework, ir. ir is designed for high throughput, integrates well with existing bioinformatics pipelines, and has much higher classification accuracy than existing methods when applied to whole genome data. ir is implemented primarily in R with core feature calculation methods written in C++. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at egana/ ir legana.fingerhut@my.jcu.edu.au ira.cooke@jcu.edu.au Supplementary data are available at egana/ _pub
A barcode of life database for the Cephalopoda? Considerations and concerns
Publisher: Springer Science and Business Media LLC
Date: 27-02-2007
The evolution and origin of tetrodotoxin acquisition in the blue-ringed octopus (genus Hapalochlaena)
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.AQUATOX.2018.10.012
Abstract: Tetrodotoxin is a potent non-proteinaceous neurotoxin, which is commonly found in the marine environment. Synthesised by bacteria, tetrodotoxin has been isolated from the tissues of several genera including pufferfish, salamanders and octopus. Believed to provide a defensive function, the independent evolution of tetrodotoxin sequestration is poorly understood in most species. Two mechanisms of tetrodotoxin resistance have been identified to date, tetrodotoxin binding proteins in the circulatory system and mutations to voltage gated sodium channels, the binding target of tetrodotoxin with the former potentially succeeding the latter in evolutionary time. This review focuses on the evolution of tetrodotoxin acquisition, in particular how it may have occurred within the blue-ringed octopus genus (Hapalochlaena) and the subsequent impact on venom evolution.
Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts
Publisher: American Association for the Advancement of Science (AAAS)
Date: 27-11-2020
Abstract: Genomes of 150 coral colonies reveal evolutionary processes related to past climatic change on the Great Barrier Reef.
Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris
Publisher: American Chemical Society (ACS)
Date: 16-09-2018
DOI: 10.1021/ACS.JPROTEOME.8B00525
Abstract: The salivary apparatus of the common octopus ( Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioral studies and molecular analysis on O. vulgaris and related species suggests that its proteome should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the posterior salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.
Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae)
Publisher: American Chemical Society (ACS)
Date: 10-01-2019
DOI: 10.1021/ACS.JPROTEOME.8B00569
Abstract: Sepioloidea lineolata, the striped pyjama squid (family Sepiadariidae), is a small species of benthic bobtail squid distributed along the Southern Indo-Pacific coast of Australia. Like other sepiadariid squids, it is known to secrete large volumes of viscous slime when stressed. In order to identify key proteins involved in the function of sepiadariid slimes, we compared the slime proteome of Sepioloidea lineolata with that of a closely related species, Sepiadarium austrinum. Of the 550 protein groups identified in Sepioloidea lineolata slime, 321 had orthologs in Sepiadarium austrinum, and the abundance of these (iBAQ) was highly correlated between species. Both slimes were dominated by a small number of abundant proteins, and several of these were short secreted proteins with no homologues outside the class Cephalopoda. No mucins were identified within either species' slime, suggesting that it is structurally distinct from mucin polymer-based gels found in many vertebrate and echinoderm secretions. The extent of N-glycosylation in the slime of Sepioloidea lineolata was also studied via glycan cleavage with Peptide: N-glycosidase F (PNGase-F). Although very few (four) proteins showed strong evidence of N-glycosylation, we found that treatment with PNGase-F led to a slight increase in peptide identification rates compared with controls.
Closely related octopus species show different spatial genetic structures in response to the Antarctic seascape
Publisher: Wiley
Date: 05-09-2017
DOI: 10.1002/ECE3.3327
Effects of controlled oxidative stress and uncouplers on primary photosynthetic processes in vegetative cells of Antarctic alga Zygnema sp.
Publisher: Masaryk University Press
Date: 2016
DOI: 10.5817/CPR2016-1-10
Abstract: In our study, we present responses of Antarctic strain of filamentous alga Zygnema sp. collected at James Ross Island (Antarctica) to application of variuos uncouplers of pri-mary photosynthetic processes. We exposed the alga to different concentrations of nigericin, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), dithiothreitol (DTT), methyl viologen (MV) and hydrogen peroxide (H2O2) in order to test stability of photosystem II, involvement of non-photochemical quenching, and PS II functioning under combination of moderate light with particular uncoupler. Oxidative stress tolerance was tested by the combination of hydrogen peroxide (H2O2) and moderate light. Time courses of FV/FM, FPSII, NPQ and qF0 were investigated and particular effects of the above-specified chem-icals discussed. Moderate doses of uncouplers allowing partial recovery, and the doses causing full inhibition of PS II were specified.
Temporal genetic patterns of diversity and structure evidence chaotic genetic patchiness in a spiny lobster.
Publisher: Wiley
Date: 09-12-2018
DOI: 10.1111/MEC.14427
Abstract: Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, postsettlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test species for chaotic genetic patchiness and selection during early benthic life. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to investigate chaotic genetic patchiness and postsettlement selection in this species. We assessed differences in genetic structure and ersity of recently settled pueruli across four settlement years and between two sites in southeast Australia separated by approximately 1,000 km. Postsettlement selection was investigated by identifying loci under putative positive selection between recently settled pueruli and postpueruli and quantifying differences in the magnitude and strength of the selection at each year and site. Genetic differences within and among sites through time in neutral SNP markers indicated chaotic genetic patchiness. Recently settled puerulus at the southernmost site exhibited lower genetic ersity during years of low puerulus catches, further supporting this hypothesis. Finally, analyses of outlier SNPs detected fluctuations in the magnitude and strength of the markers putatively under positive selection over space and time. One locus under putative positive selection was consistent at both locations during the same years, suggesting the existence of weak postsettlement selection.
Southern Ocean diversity: new paradigms from molecular ecology
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.TREE.2012.05.009
Abstract: Southern Ocean bio ersity reflects past climate, oceanographic, and tectonic changes. Molecular data from contemporary populations carry signatures of these processes. Here, we review new molecular studies on Southern Ocean benthic fauna. Many of these studies focus on species with extensive geographic or bathymetric distributions, and resolve taxonomic questions. Reviewing all available data, we show that, in addition to reflecting life-history characteristics, the molecular signals found in these studies provide an insight into how species survived the last glacial maximum (LGM). We identify molecular signatures that are characteristic of surviving glacial cycles in small refugia on the continental shelf and distinguish them from molecular signatures that are indicative of surviving glacial cycles in the deep sea.
Neotenous origins for pelagic octopuses
Publisher: Elsevier BV
Date: 04-2004
Redescription of the deep-sea octopod Benthoctopus normani (Massy 1907) and a description of a new species from the Northeast Atlantic
Publisher: Informa UK Limited
Date: 12-2006
Morphological assessment of the Octopus vulgaris species complex evaluated in light of molecular‐based phylogenetic inferences
Publisher: Wiley
Date: 20-09-2016
DOI: 10.1111/ZSC.12207
Benthoctopus rigbyae, n. sp., A New Species of Cephalopod (Octopoda; Incirrata) from Near the Antarctic Peninsula
Publisher: Institute of Malacology
Date: 03-2009
DOI: 10.4002/040.051.0102
Climatic change drives dynamic source–sink relationships in marine species with high dispersal potential
Publisher: Wiley
Date: 16-02-2021
DOI: 10.1002/ECE3.7204
Description and phylogenetic relationships of a new genus of octopus, Sasakiopus (Cephalopoda: Octopodidae), from the Bering Sea, with a redescription of Sasakiopus salebrosus (Sasaki, 1920)
Publisher: Oxford University Press (OUP)
Date: 02-2010
Related Organisations
Universidade Do Estado De Minas Gerais Unidade Carangola
Location: Brazil
University Of Oxford
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE230100180
Start Date: 2023
End Date: 12-2023
Amount: $234,438.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP120200164
Start Date: 10-2012
End Date: 09-2017
Amount: $520,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP190101347
Start Date: 2019
End Date: 12-2022
Amount: $285,000.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP180100267
Start Date: 10-2019
End Date: 10-2024
Amount: $394,015.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP110100592
Start Date: 2011
End Date: 05-2015
Amount: $225,000.00
Funder: Australian Research Council
View Funded ActivityIndustrial Transformation Research Hubs - Grant ID: IH210100014
Start Date: 09-2021
End Date: 08-2026
Amount: $4,996,503.00
Funder: Australian Research Council
View Funded ActivitySpecial Research Initiatives - Grant ID: SR200100005
Start Date: 06-2021
End Date: 06-2030
Amount: $36,000,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP150101491
Start Date: 02-2015
End Date: 12-2018
Amount: $335,100.00
Funder: Australian Research Council
View Funded Activity