Global distribution pattern and conservation of the cosmopolitan cold-water coral species Desmophyllum dianthus under climate change

Global climate change impacts marine ecosystems differently across oceanic regions and depths. Thus, understanding how widespread key species adapt globally and locally to multidimensional climate change is crucial for targeted conservation. This study focuses on the cosmopolitan cold-water coral (CWC) Desmophyllum dianthus using ecological niche models (ENMs) to explore climate adaptation and conservation strategies. The findings indicated that D. dianthus occupied a broad ecological niche but had low ecological niche overlap across populations, suggesting local adaptations and supporting population-level ENMs. The models predicted that over 80% of D. dianthus suitable habitats would persist under SSP1-2.6 and SSP5-8.5 climate scenarios by the 2100s, potentially increasing to 95% as new habitats emerge, demonstrating its robust adaptability. However, localized environmental shifts could precipitate habitat losses in areas like the Reykjanes Ridge, Rockall Plateau, Mediterranean Sea, and Patagonian Shelf. We also applied Linkage Mapper to identify potential ecological corridors that intertwined nearshore macrohabitat patches with deep-sea stepping-stone habitats such as escarpments, seamounts, and ridges, maintaining population connectivity. Despite this, the habitats and ecological corridors of D. dianthus remained largely unprotected, with vulnerable portions lying outside of marine protected areas (MPAs), thus underscoring the urgent need for more MPA. These spatial-temporal predictions provide essential insights for the conservation and management of cosmopolitan CWC D. dianthus and serve as a benchmark for the adaptive survival of similar taxa.

Ancient Hybridisation Fuelled Diversification in Acropora Corals

Introgression is the infiltration or flow of genes from one species to another through hybridisation followed by backcrossing. This may lead to incorrect phylogenetic reconstruction or divergence-time estimation. Acropora is a dominant genus of reef-building corals; however, whether this group has an introgression history before their diversification remains unclear, and previous divergence-time estimates of Acropora have not considered the impact of introgression. In this study, we broke through the limitation of a few genes and a few species and proved the existence of ancient introgression in the evolution of Acropora from whole-genome protein-coding sequences. We inferred 21.9% of all triplet loci (homologous loci from three different species) with a history of introgression and a series of introgression events with a genetic material contribution of up to 30.9% before diversification. Furthermore, 7756 nuclear loci were clustered into three groups using a multidimensional scaling algorithm, the heterogeneity of which resulted in different phylogenetic relationships. The diversification time of Acropora was estimated to be middle to late Miocene when we retained only the gene group with the lowest degree of introgression. The collision of Australia with the Pacific arcs and the Southeast Asian margin in the early Miocene, and a series of cooling events in the middle to late Miocene, may provide geographical and climatic conditions for the diversification of Acropora, respectively. Therefore, our results indicate that at the genome-wide level, ancient introgressive hybridisation may have promoted the radiation evolution of Acropora. Based on our results, the influence of introgression should be taken into account when reconstructing phylogenetic relationships and evaluating divergence time.

Climate change extinctions

Climate change is expected to cause irreversible changes to biodiversity, but predicting those risks remains uncertain. I synthesized 485 studies and more than 5 million projections to produce a quantitative global assessment of climate change extinctions. With increased certainty, this meta-analysis suggests that extinctions will accelerate rapidly if global temperatures exceed 1.5°C. The highest-emission scenario would threaten approximately one-third of species, globally. Amphibians; species from mountain, island, and freshwater ecosystems; and species inhabiting South America, Australia, and New Zealand face the greatest threats. In line with predictions, climate change has contributed to an increasing proportion of observed global extinctions since 1970. Besides limiting greenhouse gases, pinpointing which species to protect first will be critical for preserving biodiversity until anthropogenic climate change is halted and reversed.

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.

Systematic review of the uncertainty of coral reef futures under climate change

Climate change impact syntheses, such as those by the Intergovernmental Panel on Climate Change, consistently assert that limiting global warming to 1.5 °C is unlikely to safeguard most of the world's coral reefs. This prognosis is primarily based on a small subset of available models that apply similar 'excess heat' threshold methodologies. Our systematic review of 79 articles projecting coral reef responses to climate change revealed five main methods. 'Excess heat' models constituted one third (32%) of all studies but attracted a disproportionate share (68%) of citations in the field. Most methods relied on deterministic cause-and-effect rules rather than probabilistic relationships, impeding the field's ability to estimate uncertainty. To synthesize the available projections, we aimed to identify models with comparable outputs. However, divergent choices in model outputs and scenarios limited the analysis to a fraction of available studies. We found substantial discrepancies in the projected impacts, indicating that the subset of articles serving as a basis for climate change syntheses may project more severe consequences than other studies and methodologies. Drawing on insights from other fields, we propose methods to incorporate uncertainty into deterministic modeling approaches and propose a multi-model ensemble approach to generating probabilistic projections for coral reef futures.

Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species and community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this is only possible with an in-depth overview of the technological advancements and a discussion of the pros and cons of available methods. We therefore conducted a systematic literature review of 407 peer-reviewed papers on aquatic eDNA published between 2012 and 2021. We observed a gradual increase in the annual number of publications from four (2012) to 28 (2018), followed by a rapid growth to 124 publications in 2021. This was mirrored by a tremendous diversification of methods in all aspects of the eDNA workflow. For example, in 2012 only freezing was applied to preserve filter samples, whereas we recorded 12 different preservation methods in the 2021 literature. Despite an ongoing standardisation debate in the eDNA community, the field is seemingly moving fast in the opposite direction and we discuss the reasons and implications. Moreover, by compiling the largest PCR-primer database to date, we provide information on 522 and 141 published species-specific and metabarcoding primers targeting a wide range of aquatic organisms. This works as a user-friendly 'distillation' of primer information that was hitherto scattered across hundreds of papers, but the list also reflects which taxa are commonly studied with eDNA technology in aquatic environments such as fish and amphibians, and reveals that groups such as corals, plankton and algae are under-studied. Efforts to improve sampling and extraction methods, primer specificity and reference databases are crucial to capture these ecologically important taxa in future eDNA biomonitoring surveys. In a rapidly diversifying field, this review synthetises aquatic eDNA procedures and can guide eDNA users towards best practice.

Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecast future genetic offset in gradient forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming scenario (RCP 2.6), we predicted a general pattern of increasing genetic offset with latitude. Under the extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch between current allele frequencies and those required to cope with local environmental change, compared to populations in the inshore Kimberley region. The study suggests complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.