Biology subjects

Riginos, C.

Publications and source records attributed to Riginos, C..

16 recordsLinked to original sources

bioRxiv2026

A Chromosome Scale Genome Assembly for the Australian blue mussel Mytilus planulatus

Mussels belonging to the genus Mytilus are among the world's most ecologically and economically important bivalve molluscs. Although the genus most likely originated in the Northern Hemisphere, the evolutionary history of Southern Hemisphere lineages, including the timing and number of colonisation events leading to the extant Australian populations, remains debated. Limited genomic resources have hindered the reconstruction of these evolutionary histories. In Australia, distinguishing native Mytilus planulatus from invasive Mytilus galloprovincialis is critical for biosecurity and conservation, but previous molecular approaches lacked sufficient resolution to resolve species boundaries and hybridisation patterns. Here, we present the first chromosome-scale reference genome for M. planulatus. The assembly consists of 14 chromosomes and over 51,000 annotated protein-coding genes per haplotype. Comparative analysis revealed extensive structural variation and widespread hemizygosity despite a largely conserved chromosomal organisation relative to M. galloprovincialis. Population analyses using SNPs and gene presence-absence variation in resequenced individuals confirmed previously inferred patterns of population structure and establish this reference genome as a valuable resource for future studies of genome evolution, adaptation and population genomics in Mytilus.

genomics↗

bioRxiv2026

Heatwave winners and losers: cryptic coral holobionts differ in thermal tolerance

Extreme climatic events are reshaping ecosystems worldwide as individual organisms vary markedly in their ability to withstand these disturbances. Deciphering patterns of persistence on local scales is therefore critical for predicting biodiversity trajectories under intensifying climate extremes. In this study, we examined variation in thermal stress responses among individuals of the coral Stylophora pistillata species complex during a heatwave at Heron Island Reef, Australia. More than half of the focal coral colonies died on the reef, and survival of coral fragments maintained under ex situ common thermal stress conditions was significantly correlated with the survival of their source colony. This demonstrates that survival differences result largely from biological factors rather than differential thermal exposure across reef habitats. Under common garden conditions, we observed striking differences in bleaching severity and survival times among three sympatric cryptic taxa and their highly host-specific symbiont community. Within the most locally common taxon, corals from historically warmer and more seasonally variable reef habitats seem more susceptible to bleaching, contrary to expectations. Together, these results reveal how biological differences among cryptic taxa and among individuals can shape coral responses during a heatwave and advance our understanding of coral vulnerability in a rapidly warming world.

ecology↗

bioRxiv2026

Localised admixture triggers parallel adaptation in a coral species trio on the Great Barrier Reef

Hybridisation can shape evolutionary trajectories and fuel rapid adaptation. Yet, whether adaptive introgression repeatedly reconfigures genomes in predictable ways remains largely unknown. Here, we show that three-way admixture drives repeatable parallel differentiation in reef-building corals in the Acropora hyacinthus species complex. Adaptive introgression is confined to the southern Great Barrier Reef, where admixture timing coincides with a recent breakdown in species barriers despite limited historical gene flow. Genome-wide introgression is characterised by numerous shared minor-parent ancestry peaks that are enriched for stress-response genes and under positive selection for parallel adaptive admixture. Our results demonstrate that introgressive hybridisation can be geographically restricted between sympatric marine species and can promote repeated rapid adaptation that transcends species boundaries.

evolutionary biology↗

bioRxiv2026

Genomic repeatability and predictability of local (mal)adaptation in a reef-building coral

Climate change is a growing threat to biodiversity, and the persistence of populations largely depends on their capacity to adapt to changing environmental conditions. Although there is an urgent need to forecast local adaptive potential, it is unclear how such predictions are affected by the genomic architectures underlying local adaptation across a species range. In this study, we examine the genomic basis of local adaptation of the short-distance dispersing coral Stylophora pistillata, sampled at forty-six sites across eight reefs of the Great Barrier Reef, Australia. Our results show that thermal adaptation for this species involves hundreds of genomic loci with combinations that differ across geographic regions. Although adaptive loci were largely region-specific, genotype-environment relationships estimated across the entire range could predict regional-level adaptive patterns. This shows that genome-wide sequence data combined with geographically broad sampling can support reliable evolutionary forecasting. Under climate change projections, predicted shifts in genotype-environment associations were highly spatially variable, both between and within geographic regions. While some populations might be sufficiently adapted for moderate (SSP1-2.6 and SSP2-4.5) climate warming by 2050, up to 30% may face severe maladaptation risk by 2100 under a high-emission (SSP5-8.5) scenario. Collectively, these findings offer new insights into the spatial distribution of coral adaptive potential and how it might shape corals resilience in a warming ocean.

evolutionary biology↗

bioRxiv2025

Causal modelling reveals lower coral genetic diversity in more heterogenous reef environments

Conserving genetic diversity is crucial for maintaining species evolutionary potential and resilience to environmental change. Yet, directly measuring genetic diversity across large spatial scales remains resource-intensive and impractical for conservation planning. Identifying reliable, accessible, and cost-effective spatial predictors of genetic diversity would significantly enhance our ability to incorporate genetic diversity into conservation efforts. Caribbean coral reefs represent a compelling system for investigating such predictors, as these ecosystems face unprecedented threats from disease outbreaks and climate change. Here, we investigate the utility of several environmental proxies as surrogates for genetic diversity, which may be useful for conservation planning in resource- or data-poor regions. To achieve this goal, we used reduced-representation genomic sequencing to estimate intraspecific genetic diversity, and in doing so, identified two genetically distinct and sympatric cryptic coral species in the Agaricia tenuifolia species complex. We employed a causal inference approach to assess the relationships between genetic alpha diversity and habitat area and connectivity, habitat heterogeneity, and temperature. Statistical investigations revealed that increased habitat heterogeneity, derived from remotely sensed habitat maps, was associated with lower genetic diversity within coral populations, suggesting that habitat characteristics promoting species diversity may not maintain high genetic diversity within a single species. Habitat area and connectivity, and temperature have predominantly negative effects on genetic diversity with coral habitat area and connectivity showing markedly contrasting responses in two cryptic taxa. Thus, our findings reveal that context matters greatly, as results differ between cryptic species, across variables, and among spatial scales.

evolutionary biology↗

bioRxiv2025

Long-distance gene flow and contrasting population structures of reef-building corals and their algal symbionts inform adaptive potential across the Western Pacific

The genetic diversity and connectivity of reef-building coral populations are key to their survival in warming oceans. Yet our understanding of corals demographic resilience and adaptive potential is complicated by cryptic species diversity, wide geographic distributions, and complex coral-algal symbioses. To address these challenges, we investigated genetic connectivity and diversity of the broadcast-spawning coral Acropora spathulata and its associated Symbiodiniaceae across 29 reefs spanning the Great Barrier Reef, the Coral Sea, and New Caledonia, using whole-genome sequencing of 1,088 colonies. We identified four genetically distinct coral populations that diverged between 0.27 and 0.65 million years ago, likely due to geographic isolation across thousands of kilometers. These populations maintained asymmetrical gene flow along major ocean currents despite demographic isolation, and sustained large local effective population sizes ([~]2,900), supported by a high dispersal range of [~]100 km per generation. In contrast, their Symbiodiniaceae partners varied over finer spatial scales, with five distinct Cladocopium taxa distributed along latitudinal and cross-shore gradients, likely driven by local environmental conditions. These results suggest that high dispersal capacity and large local population size promote demographic resilience within reef systems, while environment-specific symbioses and long-distance gene flow across reef-systems support adaptation and evolutionary rescue.

molecular biology↗

bioRxiv2025

Drivers of genetic diversity across the marine tree of life

Why do some species have more genetic diversity than others? This question is one of the greatest remaining mysteries in evolutionary biology, yet we still know little about what factors predict genetic diversity among species. Efforts to quantify diversity or understand its distribution have been hampered by a lack of genomic data analyzed in a consistent way with statistical approaches that can move beyond the population level to generate species-wide estimates of genetic diversity. We address this critical gap by generating standardized estimates of genomic-level genetic diversity for 93 species sampled over 9,000 localities. Because marine species have evolved a strikingly diverse array of biological traits that have long been hypothesized to affect species-level genetic diversity, we focus our study on marine taxa. For each species, we aggregated biotic traits related to life history and abiotic features of the species range. We show that genetic diversity increases with species range extent and planktonic dispersal. We hypothesize that these traits increase a species ability to avoid or recover from bottlenecks, thereby maintaining genetic diversity. Our findings provide insights into how biotic and abiotic factors interact to shape genomic variation in the ocean, and offer a predictive framework for understanding marine biodiversity in the face of global change. Significance statementSpecies exhibit vast trait diversity that allows populations to persist. However, diversity in these traits -- e.g., how organisms reproduce, disperse, and feed -- is not easily linked to what is known of genomic diversity, even in well-studied organisms. We investigate a diverse assemblage of marine species to begin to build a predictive framework for how species traits drive genomic diversity across the worlds oceans. We find that species with larger geographic ranges have higher genomic diversity. More dispersive species also harbor higher diversity, suggesting that greater dispersal facilitates resilience to environmental change. As available datasets increase, our ability to understand fundamental links between trait and genetic diversity and how they shape species responses to environmental change will continue to improve.

evolutionary biology↗

bioRxiv2025

A rapidly closing window for coral persistence under global warming

Summary paragraphCoral reefs around the world are threatened by recurrent marine heatwaves causing mass coral bleaching and mortality1. Mitigating future warming impacts requires strategic management2 that adopts a long-term lens. Global analyses of projected heatwaves3,4 are critical for decision-making but how disturbance refugia, coral life-histories and adaptation interact with warming is unknown. Here, we simulate coral eco-evolutionary dynamics across >3,800 individual reefs of Australias iconic Great Barrier Reef under the current suite of climate projections5. We forecast a rapid coral decline before mid-century regardless of emissions scenario. Under the most likely warming6, corals may continue to decline throughout the century. However, corals may recover after mid-century provided that warming is sufficiently slow, allowing thermal adaptation to keep pace with temperature changes - as projected if warming does not exceed 2{degrees}C. Higher emission scenarios would drive most reefs to a near collapse. Future resilient reefs were mostly found in bleaching refugia, which also possessed a greater diversity of thermal phenotypes. Although cool-adapted corals disperse to thermal hotspots, there was no evidence of gene swamping undermining thermal adaptation. While opportunities exist to build management strategies that promote adaptation in thermal refugia and warm spots, curbing the rate of warming by 2050 is crucial for coral persistence.

ecology↗

bioRxiv2024

A novel framework for assessing the robustness of genomic animal models applied to a wild marine fish

In highly dispersive taxa, gene flow can homogenise genetic variation over broad spatial and temporal scales. However, phenotypic differentiation can still arise when heritable genetic variation is available to selection and (or) when organisms exhibit plasticity. Disentangling heritable versus non-heritable components of variation is possible using genomic animal models, but this approach has been underused in wild organisms. We investigated head shape variation in the marine cryptobenthic fish Bathygobius cocosensis, a highly dispersive species occupying heterogeneous environments. Head shape, a diet-related trait, is spatially structured in Australian populations. We curated a unique dataset comprising genotypic, phenotypic, and environmental variation to: (1) contrast the scales over which genetic and phenotypic variation are structured; and (2) quantify heritable versus non-heritable contributions to head shape variation using genomic animal models and comparisons between FST, PST, and QST. At macrogeographic scales (hundreds of kilometres) and over time (2 years), phenotypic differentiation (0.0001 [≤] PST [≤] 0.47) exceeded both genomic and additive genetic differentiation (0.001 [≤] FST[≤] 0.004 and 0.00001 [≤] QST [≤] 0.004, respectively). This suggests head shape variation may primarily reflect (non-heritable) plastic responses, rather than (heritable) adaptive genetic changes in mean head shape. At microgeographic scales, associations between head shape and tide pool variables were temporally variable, indicating that local environmental conditions may structure phenotypes within populations. Overall, this study highlights the value of genomic animal models for disentangling heritable and non-heritable components of phenotypic variation in dispersive marine taxa. It provides an integrative analysis linking genetic, phenotypic, and environmental variation in a cryptobenthic fish, highlighting how phenotypic divergence can emerge without strong genetic differentiation, and challenging the common assumption that phenotypic divergence necessarily implies adaptation.

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

Gene flow throughout the evolutionary history of a polymorphic and generalist clownfish

Even seemingly homogeneous on the surface, the oceans display high environmental heterogeneity across space and time. Indeed, different soft barriers structure the marine environment, which offers an appealing opportunity to study various evolutionary processes such as population differentiation and speciation. Here, we focus on Amphiprion clarkii (Actinopterygii; Perciformes), the most widespread of clownfishes that exhibits the highest colour polymorphism. Clownfishes can only disperse during a short pelagic larval phase before their sessile adult lifestyle, which might limit connectivity among populations, thus facilitating speciation events. Consequently, the taxonomic status of A. clarkii has been under debate. We used whole-genome resequencing data of 67 A. clarkii specimens spread across the Indian and Pacific Oceans to characterise the species population structure, demographic history, and colour polymorphism. We found that A. clarkii spread from the Indo-Pacific Ocean to the Pacific and Indian Oceans following a stepping-stone dispersal and that gene flow was pervasive throughout its demographic history. Moreover, edge populations exhibited more similar colouration patterns compared to central populations. However, we demonstrate that colour polymorphism is not associated with population structure, thus, colour phenotype is unreliable in assessing the taxonomic status of A. clarkii. Our study further highlights the power of whole-genome comparative studies to determine the taxonomy of geographically wide-ranging and phenotypically diverse species, supporting the status of A. clarkii as a single species.

evolutionary biology↗

bioRxiv2023

High germline mutation rates but not extreme population size outbreaks influence genetic diversity in crown-of-thorns sea stars

Lewontins paradox, the observation that levels of genetic diversity ({pi}) among animals do not scale linearly with variation in census population sizes (Nc), is an evolutionary conundrum, where the most extreme mismatches between {pi} and Nc are found for highly abundant marine invertebrates. Yet, whether new mutations influence {pi} relative to extrinsic processes remains unknown for most taxa. Here, we provide the first direct germline mutation rate () estimate for a marine invertebrate, using high-coverage (60x) whole-genome sequencing of wild-caught Acanthaster cf. solaris crown-of-thorns sea stars (Echinodermata). We also provide empirical estimates of adult Nc in Australias Great Barrier Reef to jointly examine the determinants of {pi}. Based on direct observations of 63 de novo mutations across 14 parent-offspring trios, the A. cf. solaris mean was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08). This value exceeds estimates for other invertebrates, showing greater concordance with reported vertebrate germline mutation rates. Lower-than-expected Ne ([~]70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated significant genetic drift and weak influences of contemporary population outbreaks on long-term {pi}. Our findings of elevated and low Ne in A. cf. solaris may help explain high mutational loads and extreme polymorphism levels observed in some marine invertebrate taxa and are consistent with evolving in response to Ne (drift-barrier hypothesis). This study advances our understanding of the processes controlling levels of natural genetic variation and provides new data valuable for further testing hypotheses about mutation rate evolution across animal phyla.

evolutionary biology↗

bioRxiv2022

Metadata preservation and stewardship for genomic data is possible, but must happen now

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

bioinformatics↗

bioRxiv2021

Selecting species for restoration in foundational assemblages

O_LIHumans have long sought to restore species, but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests that are increasingly threatened by environmental change. C_LIO_LIWe propose a two-part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it takes precaution against loss by ensuring an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence--e.g., abundance, species range and tolerance to environmental change. C_LIO_LIUsing existing phenotypic trait and ecological characteristic data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the worlds southern-most coral reef which naturally harbors low coral diversity to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and may be improved by including species with different traits. C_LIO_LISynthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the approach enables the functional goals of restoration to vary depending on environmental context, stakeholder values, and the spatial and temporal scales at which meaningful impacts can be achieved. C_LI

ecology↗

bioRxiv2019

genomalicious: serving up a smorgasbord of R functions for population genomic analyses

Turning SNP data into biologically meaningful results requires considerable computational acrobatics, including importing, exporting, and manipulating data among different analytical packages and programming environments, and finding ways to visualise results for data exploration and presentation. I present GENOMALICIOUS, an R package designed to provide a selection of functions for population genomicists to simply, intuitively, and flexibly, guide SNP data through their analytical pipelines, within and outside R. At the core of the original GENOMALICIOUS workflow is the conversion of genomic variant data into a data.table object. This provides a useful way of storing large amounts of data in an intuitive format that can be easily manipulated using methods unique to this object class. Over time, GENOMALICIOUS has grown to cater to a range of analyses in population structure and demography, adaptive evolution, quantitative traits, and phylogenetics. Researchers using pooled allele frequencies, or individually sequenced genotypes, are sure to find functions that accommodate their tastes in GENOMALICIOUS. The simplicity and accessibility of pipelines in GENOMALICIOUS may also serve as a useful tool for teaching basic population genetics and genomics in an R environment. The source code and a series of tutorials for this package are freely available on GitHub

bioinformatics↗

bioRxiv2018

Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals

AimWidespread coral bleaching, crown-of-thorns seastar outbreaks, and tropical storms all threaten foundational coral species of the Great Barrier Reef, with impacts differing over time and space. Yet, dispersal via larval propagules could aid reef recovery by supplying new settlers and enabling the spread of adaptive variation among regions. Documenting and predicting spatial connections arising from planktonic larval dispersal in marine species, however, remains a formidable challenge.\n\nLocationThe Great Barrier Reef, Australia\n\nMethodsContemporary biophysical larval dispersal models were used to predict longdistance multigenerational connections for two common and foundational coral species (Acropora tenuis and Acropora millepora). Spatially extensive genetic surveys allowed us to infer signatures of asymmetric dispersal for these species and evaluate concordance against expectations from biophysical models using coalescent genetic simulations, directions of inferred gene flow, and spatial eigenvector modelling.\n\nResultsAt long distances, biophysical models predicted a preponderance of north to south connections and genetic results matched these expectations: coalescent genetic simulations rejected an alternative scenario of historical isolation; the strongest signals of inferred gene flow were from north to south; and asymmetric eigenvectors derived from north to south connections in the biophysical models were significantly better predictors of spatial genetic patterns than eigenvectors derived from symmetric null spatial models.\n\nMain conclusionsResults are consistent with biophysical dispersal models yielding approximate summaries of past multigenerational gene flow conditioned upon directionality of connections. For A. tenuis and A. millepora, northern and central reefs have been important sources to downstream southern reefs over the recent evolutionary past and should continue to provide southward gene flow. Endemic genetic diversity of southern reefs suggests substantial local recruitment and lack of long distance gene flow from south to north.

ecology↗