Biology subjects

Strugnell, J. M.

Publications and source records attributed to Strugnell, J. M..

10 recordsLinked to original sources

bioRxiv2026

Enhanced survival and lower growth in assisted gene flow corals during a marine heatwave driven by local adaptation

Recent increases in the frequency of mass coral bleaching and mortality events have caused shifts in species composition and rapid global reef decline. Genetic-based techniques, like assisted gene flow (AGF), offer the potential to enhance corals climate readiness by introducing genetic variation associated with heat tolerance into vulnerable populations. This method remains untested in the wild during a marine heatwave. To this end, we selectively bred AGF corals by crossing parent Acropora tersa corals collected across five Great Barrier Reef (GBR) locations spanning a thermal and bleaching gradient. Breeding produced intra- and inter-regional offspring that were then deployed to a central GBR reef. This deployment reef was subsequently hit by a marine heatwave (>31.4{degrees}C for 17 days and >6 Degree Heating Weeks). Heat tolerance-associated traits (survival, growth, and bleaching) were compared between AGF offspring and a native control cross over the 95 days in the wild. Overall, AGF offspring had 4x greater odds of survival compared to controls, and 2x greater odds compared to northern juveniles. Growth rates were 14% higher in control juveniles compared to the mean growth rate across all AGF crosses. Interestingly, heat-stress assays (32{degrees}C) of the parental adult corals showed similar patterns to their offspring, with higher survival and lower bleaching of corals from warmer northern reefs. Taken together, these findings providing critical support that the selective breeding of AGF corals can provide enhanced survival under marine heatwave conditions in the wild. It also suggests further evaluation is needed for trait-specific responses to effectively match donor and recipient reefs in restoration planning.

ecology↗

bioRxiv2024

Chromosome-scale genome assembly the tropical abalone (Haliotis asinina)

Abalone (family Haliotidae) are an ecologically and economically significant group of marine gastropods that can be found in tropical and temperate waters. To date, only a few Haliotis genomes are available, all belonging to temperate species. Here, we provide the first reference genome of the tropical abalone Haliotis asinina. The combination of PacBio long-read HiFi sequencing and Dovetails Omni-C sequencing allowed the chromosome-level assembly of this genome, while PacBio Isoform sequencing across five tissue types enabled the construction of high-quality gene models. This assembly resulted in 16 pseudo-chromosomes spanning over 1.12 Gb (98.1% of total scaffolds length), N50 of 67.09 Mb, the longest scaffold length of 105.96 Mb, and a BUSCO completeness score of 97.6%. This study identified 25,422 protein-coding genes and 61,149 transcripts. In an era of climate change and ocean warming, this genome of a heat-tolerant species can be used for comparative genomics with a focus on thermal resistance. This high-quality reference genome of H. asinina is a valuable resource for aquaculture, fisheries, and ecological studies.

genomics↗

bioRxiv2024

Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef

The future survival of coral reefs in the Anthropocene depends on the capacity of corals to adapt as oceans warm and extreme weather events become more frequent. Targeted interventions designed to assist evolutionary processes in corals require a comprehensive understanding of the distribution and structure of standing variation, however, efforts to map genomic variation in corals have so far focussed almost exclusively on SNPs, overlooking structural variants that have been shown to drive adaptive processes in other taxa. Here we show that the reef-building coral, Acropora kenti (syn. tenuis) harbors at least five large, highly polymorphic structural variants, all of which exhibit signatures of strongly suppressed recombination in heterokaryotypes, a feature commonly associated with chromosomal inversions. Based on their high minor allele frequency, uniform distribution across habitats, and elevated genetic load, we propose that these inversions in A. kenti are likely to be under balancing selection. An excess of SNPs with high impact on protein coding genes within these loci elevates their importance both as potential targets for adaptive selection and as contributors to genetic decline if coral populations become fragmented or inbred in future.

evolutionary biology↗

bioRxiv2023

Environmental determinants of suitable habitat and the prediction of a southern shift in the future distribution of spiny lobsters, genus Jasus

Climate change is altering environmental conditions which is affecting species habitats globally. As a result, many species are shifting their habitat ranges poleward to ensure that they remain within their optimal thermal range. On average, marine species have shifted their ranges poleward by approximately 72km to track their optimal thermal conditions compared to 17km for terrestrial species. These range shifts are pushing some species out of their currently fished areas. This will require nations and fishery companies to predict the most likely areas their target species could move to and obtain permits to fish in those new areas. Spiny lobsters (genus Jasus) are likely to shift their ranges poleward as they are distributed within a relatively tight latitudinal band, but there is limited information about the extent of any potential range shifts. The aims of this study were to identify the environmental variables that characterise the current habitat locations of lobsters within the genus Jasus, and to predict their potential distribution by modelling future suitable habitat under the RCP45, RCP60, and RCP85 climate scenarios using MaxEnt. There were 16 environmental variables used for modelling suitable habitat for the present (2000-2014), while only four environmental variables were available for modelling in two future time periods (2040-2050 and 2090-2100). There was a predicted overall southern shift in suitable habitat locations for all species. The most important environmental variable identified for species distributed along continental shelves (J. edwardsii and J. lalandii) was benthic temperature. Benthic nutrients (silicate, nitrate, and phosphate) were the most important variables for species distributed around islands and on seamounts (J. paulensis, J. frontalis, and J. tristani). Approximately 90% of Jasus lobsters present range contained highly suitable habitat locations. The percent of highly suitable locations under the RCP45 and RCP60 scenarios were higher than the present percentages for each species, while under the RCP85 scenario, there was a decrease of highly suitable habitat for most species in 2040-2050 period, while for the 2090- 2100 period, there was an increase in the percent of highly suitable habitats. This study provides evidence that Jasus populations might become more abundant in the southern extents of their current range as they track their optimum habitat conditions.

ecology↗

bioRxiv2023

Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial Period

The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories and its tipping point may even lie within the mitigated warming scenarios of 1.5-2 {degrees}C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates, including the Last Interglacial, when global sea levels were 5-10 m higher than today, and global average temperatures of 0.5-1.5 {degrees}C warmer than preindustrial levels, 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. One-Sentence SummaryHistorical gene flow in marine animals indicate the West Antarctic Ice Sheet collapsed during the Last Interglacial.

evolutionary biology↗

bioRxiv2022

Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum

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) 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 divergence 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.

evolutionary biology↗

bioRxiv2020

ampir: an R package for fast genome-wide prediction of antimicrobial peptides

SummaryAntimicrobial 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, 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 Implementationampir 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 Contactlegana.fingerhut@my.jcu.edu.au; ira.cooke@jcu.edu.au Supplementary informationSupplementary data are available at https://github.com/legana/amp_pub

bioinformatics↗

bioRxiv2020

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

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 diverse 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.

genomics↗

bioRxiv2019

Global drivers of diversification in a marine species complex

Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence before speciation. The processes influencing species diversification 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 divergence, 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{degrees}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 divergence of species within the genus Jasus providing the first empirical study of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

evolutionary biology↗

bioRxiv2019

Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex

Many 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 the O. vulgaris group. 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 discordance between mitochondrial and nuclear markers; genome-wide nuclear loci supported O. vulgaris sensu stricto and Type III (South Africa) as distinct species, which mtDNA failed to recognise. Our finding of conflicting phylogenetic signal between mitochondrial and nuclear markers has broad implications for many taxa. Improved phylogenetic resolution of O. vulgaris has significant implications for appropriate management of the group and will allow greater accuracy in global fisheries catch statistics.

molecular biology↗