Two new pygmy squid from the Ryukyu archipelago, Japan, are described: Kodama jujutsu, n. gen., n... more Two new pygmy squid from the Ryukyu archipelago, Japan, are described: Kodama jujutsu, n. gen., n. sp. and Idiosepius kijimuna, n. sp. They differ from all other nominal species in a combination of traits, including the number of tentacular club suckers, shape of the funnel-mantle locking-cartilage, modification of the male hectocotylus and the structure of the gladius and nuchal-locking cartilage, in addition to mitochondrial DNA markers (12S, 16S and COI). They are both known from Okinawa Island and there is some overlap in their distributions. In a molecular phylogeny that includes all nominal Idiosepiidae, Kodama jujutsu, n. gen., n. sp. is sister taxon to a clade containing Xipholeptos Reid & Strugnell, 2018 and Idiosepius Steenstrup, 1881. Xipholeptos and Idiosepius are sister taxa. Idiosepius spp. now includes seven nominal species. In addition, aspects of the behaviour of the new species are described.
Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland r... more Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure i...
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bl... more 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 divergence since the last glacial maximum (LGM) ...
While there is now strong evidence that many factors can shape dispersal, the mechanisms influenc... more While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species‐specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual‐based model couple...
Background Cephalopods represent a rich system for investigating the genetic basis underlying org... more Background Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse 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. Findings 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. Examin...
Abstract The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species ext... more Abstract The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce “South Sea” pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result genetic tools that can be readily implemented into breeding programs have been developed. However, to date there is no routine single nucleotide polymorphism (SNP) pedigree reconstruction tool publicly available. In this study, we isolated and assessed a panel of 934 genome-wide DArTcap™ SNPs for their utility and discriminatory power in resolving pedigree relationships in P. maxima. The panel was assessed for its power to assign parentage through in silico simulations of 1,000 progeny in a mass-spawning scenario, based on genotypes of 100 broodstock (1:1 sex ratio) and allowing for random missing genotypes in individuals (0–40%). Assignment success was then assessed across various pedigree panel sizes (25–934 SNPs ranked from the highest minor allele frequency). Simulations showed that a SNP panel comprising 50 or more SNPs had high pedigree resolution and the power to correctly assign progeny to a parent-progeny trio with 95 % confidence. In the simulation examining the effect of missing genotypes on assignment success, even where 40 % of alleles were missing in individuals only 150 SNPs were required in the panel to accurately assign parentage. Progeny from a commercial hatchery mass spawn involving 184 candidate parents were also assigned to their parents using the SNP panel and identified 79 full-sib families and genetic contributions from 33 sires and 11 dams. A highly skewed representation of family distributions in the cohort was observed which highlights the challenge of using a mass-spawning approach to the capture and identification of genetic diversity in P. maxima breeding programs.
Eradicating invasive species is difficult, but success is more likely when populations are small ... more Eradicating invasive species is difficult, but success is more likely when populations are small after arrival. The cane toad, Rhinella marina, is an invasive pest species that threatens native fauna worldwide. Increasingly, environmental DNA (eDNA) is used as a technique to monitor the presence of invasive species given its power to detect low numbers of individuals. We aimed to investigate eDNA persistence in freshwater at three different temperatures (25, 30 and 35°C) and eDNA detection thresholds for R. marina using controlled experiments in aquaria. For the latter, two water volumes and two cane toad exposure times were used (800 or 200 L volume with 5 or 30 min exposure). A 15‐ml water sample was collected from each replicated aquaria and preserved with 5 ml Longmire's buffer. Environmental DNA was extracted and four technical quantitative PCR replicates were analyzed targeting the cane toad 16S rDNA mitochondrial gene. Environmental DNA decayed rapidly in water and was re...
Summary Antimicrobial peptides (AMPs) are the key components of the innate immune system that pro... more Summary 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, ampir. ampir 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. Availability and implementation ampir 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 https://github.com/legana/ampir. Supplementary information Supp...
The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America ... more The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America and caused the separation of the Western Atlantic and Eastern Pacific oceans, resulting in profound changes in the environmental and oceanographic conditions. To evaluate how these changes have influenced speciation processes in octopods, fragments of two mitochondrial (Cytochrome oxidase subunit I, COI and 16S rDNA) and two nuclear (Rhodopsin and Elongation Factor-1α, EF-1α) genes were amplified from samples from the Atlantic and Pacific oceans. One biogeographical and four fossil calibration priors were used within a relaxed Bayesian phylogenetic analysis framework to estimate divergence times among cladogenic events. Reconstruction of the ancestral states in phylogenies was used to infer historical biogeography of the lineages and species dispersal routes. The results revealed three well-supported clades of transisthmian octopus sister species pair/complex (TSSP/TSSC) and two addition...
Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc wit... more Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated...
ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic spec... more ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic species complexes. Mitochondrial markers are ubiquitously used to address phylogeographic questions, and have been used to identify some cryptic species complexes; however, their efficacy in inference of evolutionary processes in the nuclear genome has not been thoroughly investigated. We used double digest restriction site-associated DNA sequencing (ddRADseq) markers to quantify species boundaries in the widely distributed and high value common octopus,Octopus vulgaris, comparing genome-wide phylogenetic signal to that obtained from mitochondrial markers. Phylogenetic analyses, genome-wide concordance and species tree estimation based on 604 genome-wide ddRADseq loci revealed six species within theO. vulgarisgroup. Divergence time estimates suggested modern-day species evolved over the last 2.5 ma, during a period of global cooling. Importantly, our study identified significant phylogenetic...
Two new pygmy squid from the Ryukyu archipelago, Japan, are described: Kodama jujutsu, n. gen., n... more Two new pygmy squid from the Ryukyu archipelago, Japan, are described: Kodama jujutsu, n. gen., n. sp. and Idiosepius kijimuna, n. sp. They differ from all other nominal species in a combination of traits, including the number of tentacular club suckers, shape of the funnel-mantle locking-cartilage, modification of the male hectocotylus and the structure of the gladius and nuchal-locking cartilage, in addition to mitochondrial DNA markers (12S, 16S and COI). They are both known from Okinawa Island and there is some overlap in their distributions. In a molecular phylogeny that includes all nominal Idiosepiidae, Kodama jujutsu, n. gen., n. sp. is sister taxon to a clade containing Xipholeptos Reid & Strugnell, 2018 and Idiosepius Steenstrup, 1881. Xipholeptos and Idiosepius are sister taxa. Idiosepius spp. now includes seven nominal species. In addition, aspects of the behaviour of the new species are described.
Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland r... more Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure i...
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bl... more 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 divergence since the last glacial maximum (LGM) ...
While there is now strong evidence that many factors can shape dispersal, the mechanisms influenc... more While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species‐specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual‐based model couple...
Background Cephalopods represent a rich system for investigating the genetic basis underlying org... more Background Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse 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. Findings 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. Examin...
Abstract The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species ext... more Abstract The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce “South Sea” pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result genetic tools that can be readily implemented into breeding programs have been developed. However, to date there is no routine single nucleotide polymorphism (SNP) pedigree reconstruction tool publicly available. In this study, we isolated and assessed a panel of 934 genome-wide DArTcap™ SNPs for their utility and discriminatory power in resolving pedigree relationships in P. maxima. The panel was assessed for its power to assign parentage through in silico simulations of 1,000 progeny in a mass-spawning scenario, based on genotypes of 100 broodstock (1:1 sex ratio) and allowing for random missing genotypes in individuals (0–40%). Assignment success was then assessed across various pedigree panel sizes (25–934 SNPs ranked from the highest minor allele frequency). Simulations showed that a SNP panel comprising 50 or more SNPs had high pedigree resolution and the power to correctly assign progeny to a parent-progeny trio with 95 % confidence. In the simulation examining the effect of missing genotypes on assignment success, even where 40 % of alleles were missing in individuals only 150 SNPs were required in the panel to accurately assign parentage. Progeny from a commercial hatchery mass spawn involving 184 candidate parents were also assigned to their parents using the SNP panel and identified 79 full-sib families and genetic contributions from 33 sires and 11 dams. A highly skewed representation of family distributions in the cohort was observed which highlights the challenge of using a mass-spawning approach to the capture and identification of genetic diversity in P. maxima breeding programs.
Eradicating invasive species is difficult, but success is more likely when populations are small ... more Eradicating invasive species is difficult, but success is more likely when populations are small after arrival. The cane toad, Rhinella marina, is an invasive pest species that threatens native fauna worldwide. Increasingly, environmental DNA (eDNA) is used as a technique to monitor the presence of invasive species given its power to detect low numbers of individuals. We aimed to investigate eDNA persistence in freshwater at three different temperatures (25, 30 and 35°C) and eDNA detection thresholds for R. marina using controlled experiments in aquaria. For the latter, two water volumes and two cane toad exposure times were used (800 or 200 L volume with 5 or 30 min exposure). A 15‐ml water sample was collected from each replicated aquaria and preserved with 5 ml Longmire's buffer. Environmental DNA was extracted and four technical quantitative PCR replicates were analyzed targeting the cane toad 16S rDNA mitochondrial gene. Environmental DNA decayed rapidly in water and was re...
Summary Antimicrobial peptides (AMPs) are the key components of the innate immune system that pro... more Summary 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, ampir. ampir 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. Availability and implementation ampir 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 https://github.com/legana/ampir. Supplementary information Supp...
The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America ... more The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America and caused the separation of the Western Atlantic and Eastern Pacific oceans, resulting in profound changes in the environmental and oceanographic conditions. To evaluate how these changes have influenced speciation processes in octopods, fragments of two mitochondrial (Cytochrome oxidase subunit I, COI and 16S rDNA) and two nuclear (Rhodopsin and Elongation Factor-1α, EF-1α) genes were amplified from samples from the Atlantic and Pacific oceans. One biogeographical and four fossil calibration priors were used within a relaxed Bayesian phylogenetic analysis framework to estimate divergence times among cladogenic events. Reconstruction of the ancestral states in phylogenies was used to infer historical biogeography of the lineages and species dispersal routes. The results revealed three well-supported clades of transisthmian octopus sister species pair/complex (TSSP/TSSC) and two addition...
Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc wit... more Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated...
ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic spec... more ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic species complexes. Mitochondrial markers are ubiquitously used to address phylogeographic questions, and have been used to identify some cryptic species complexes; however, their efficacy in inference of evolutionary processes in the nuclear genome has not been thoroughly investigated. We used double digest restriction site-associated DNA sequencing (ddRADseq) markers to quantify species boundaries in the widely distributed and high value common octopus,Octopus vulgaris, comparing genome-wide phylogenetic signal to that obtained from mitochondrial markers. Phylogenetic analyses, genome-wide concordance and species tree estimation based on 604 genome-wide ddRADseq loci revealed six species within theO. vulgarisgroup. Divergence time estimates suggested modern-day species evolved over the last 2.5 ma, during a period of global cooling. Importantly, our study identified significant phylogenetic...
Uploads