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

Forecasting habitat suitability and niche shifts of two global maize pests: Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae)

BACKGROUND

Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB) are devastating pests of the agricultural crop maize worldwide. However, little is known about their potential distribution and niche shifts during their global invasion. Since long-term selection to past climate variability has shaped their historical niche breadth, such niche shifts may provide an alternative basis for understanding their responses to present and future climate change. By integrating the niche unfilling, stability, and expansion situations into a single framework, our study quantifies the patterns of niche shift in the spatial distribution of these two pests during the different periods.

RESULTS

Our results show that the overall suitable habitats of ACB and ECB in the future decrease but highly and extremely suitable habitat will become more widespread, suggesting these two insects may occur more frequently in specific regions. Compared with Southeast Asia and Australia, the ACB niche in China exhibited expansion rather than unfilling. For ECB, initial niches have a tendency to be retained in Eurasia despite there also being potential for expansion in North America. The niche equivalency and similarity test results further indicate that niche shifts were common for both ACB and ECB in different survival regions during their colonization of new habitat and their suitable habitat changes during the paleoclimate were associated with climatic changes.

CONCLUSIONS

These findings improve our understanding of the ecological characteristics of ACB and ECB worldwide, and will be useful in the development of prevention and control strategies for two insect pests worldwide. © 2024 Society of Chemical Industry.

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, harbours 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.

Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp

Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.

Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data

Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.

Genome-wide analysis to uncover how Pocillopora acuta survives the challenging intertidal environment

Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls. However, the intertidal section of coastal armour is a challenging environment for corals, with conditions during periods of emersion being particularly stressful. Here, we scanned the entire genome of P. acuta corals to identify the regions harbouring single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) that separate intertidal colonies (n = 18) from those found in subtidal areas (n = 21). Findings revealed 74,391 high quality SNPs distributed across 386 regions of the P. acuta genome. While the majority of the detected SNPs were in non-coding regions, 12% were identified in exons (i.e. coding regions). Functional SNPs that were significantly associated with intertidal colonies were found in overrepresented genomic regions linked to cellular homeostasis, metabolism, and signalling processes, which may represent local environmental adaptation in the intertidal. Interestingly, regions that exhibited CNVs were also associated with metabolic and signalling processes, suggesting P. acuta corals living in the intertidal have a high capacity to perform biological functions critical for survival in extreme environments.

Resilience to periodic disturbances and the long-term genetic stability in Acropora coral

Climate change is restructuring natural ecosystems. The direct impacts of these events on biodiversity and community structure are widely documented, but the impacts on the genetic variation of populations remains largely unknown. We monitored populations of Acropora coral on a remote coral reef system in northwest Australia for two decades and through multiple cycles of impact and recovery. We combined these demographic data with a temporal genetic dataset of a common broadcast spawning corymbose Acropora to explore the spatial and temporal patterns of connectivity underlying recovery. Our data show that broad-scale dispersal and post-recruitment survival drive recovery from recurrent disturbances, including mass bleaching and mortality. Consequently, genetic diversity and associated patterns of connectivity are maintained through time in the broader metapopulation. The results highlight an inherent resilience in these globally threatened species of coral and showcase their ability to cope with multiple disturbances, given enough time to recover is permitted.

Finding genes and pathways that underlie coral adaptation

Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies.

Exploring coral speciation: Multiple sympatric Stylophora pistillata taxa along a divergence continuum on the Great Barrier Reef

Understanding how biodiversity originates and is maintained are fundamental challenge in evolutionary biology. Speciation is a continuous process and progression along this continuum depends on the interplay between evolutionary forces driving divergence and forces promoting genetic homogenisation. Coral reefs are broadly connected yet highly heterogeneous ecosystems, and divergence with gene flow at small spatial scales might therefore be common. Genomic studies are increasingly revealing the existence of closely related and sympatric taxa within taxonomic coral species, but the extent to which these taxa might still be exchanging genes and sharing environmental niches is unclear. In this study, we sampled extensively across diverse habitats at multiple reefs of the Great Barrier Reef (GBR) and comprehensively examined genome-wide diversity and divergence histories within and among taxa of the Stylophora pistillata species complex. S. pistillata is one of the most abundant and well-studied coral species, yet we discovered five distinct taxa, with wide geographic ranges and extensive sympatry. Demographic modelling showed that speciation events have occurred with gene flow and that taxa are at different stages along a divergence continuum. We found significant correlations between genetic divergence and specific environmental variables, suggesting that niche partitioning may have played a role in speciation and that S. pistillata taxa might be differentially adapted to different environments. Conservation actions rely on estimates of species richness, population sizes and species ranges, which are biased if divergent taxa are lumped together. As coral reefs are rapidly degrading due to climate change, our study highlights the importance of recognising evolutionarily distinct and differentially adapted coral taxa to improve conservation and restoration efforts aiming at protecting coral genetic diversity.