Genome-wide sequencing identifies a thermal-tolerance related synonymous mutation in the mussel, Mytilisepta virgata

Cell death and antioxidant responses in Mytilus galloprovincialis under heat stress: Evidence of genetic loci potentially associated with thermal resilience

The global seawater temperature is expected to further rise in the following years. While species have historically adapted to climatic variations, the current pace of climate change may exceed their ability to adapt. The abnormally increased seawater temperatures occasionally lead to high mortalities of marine bivalve mollusks, threatening the productivity of aquaculture and the sustainability of wild populations. This study investigates the antioxidant and cell death mechanisms of the Mediterranean mussel Mytilus galloprovincialis during a 25-day exposure to temperatures of 24°C, 26°C, and 28°C, by analyzing the transcription of key genes and assessing the oxidative damage on days 1, 3, 12, and 25. In addition, individuals resilient (survived at 28°C until day 30) and susceptible (died early at 26°C and 28°C) to thermal stress were collected to investigate potential polymorphisms in associated genes. The results showed increased transcription of antioxidant genes at higher temperatures. Elevated pro-apoptotic indices were initially observed at 26°C and a higher mortality than at 28°C. However, final mortality was much higher at 28°C. At 26°C, mussels exhibited the highest oxidative damage and pro-apoptotic indices after 25 days. At 28°C, although oxidative damage occurred after 24 hours, survivors maintained a prolonged activated antioxidant defense and increased lc3b transcription, which likely contributed to the observed reduction of pro-apoptotic and oxidative damage metrics on day 25, compared to 26°C. Further, the coding sequences of catalase, intracellular Cu-Zn superoxide dismutase (Cu-Zn sod), and fas-associated protein with death domain (fadd) from heat-resilient and heat-susceptible mussels were analyzed. Based on statistical correlation of nucleotide and genotype frequencies with resilience phenotypes, two novel single nucleotide polymorphisms (SNPs) in Cu-Zn sod and one in fadd were detected, potentially correlating with thermal stress resilience. These findings offer valuable insights into the physiological and genetic adaptations of M. galloprovincialis to rising temperatures and highlight loci potentially linking to thermal resilience.

Toward a Global Science of Conservation Genomics: Coldspots in Genomic Resources Highlight a Need for Equitable Collaborations and Capacity Building

Advances in genomic sequencing have magnified our understanding of ecological and evolutionary mechanisms relevant to biodiversity conservation. As a result, the field of conservation genomics has grown rapidly. Genomic data can be effective in guiding conservation decisions by revealing fine-scale patterns of genetic diversity and adaptation. Adaptive potential, sometimes referred to as evolutionary potential, is particularly informative for conservation due to its inverse relationship with extinction risk. Yet, global coldspots in genomic resources impede progress toward conservation goals. We undertook a systematic literature review to characterise the global distribution of genomic resources for amphibians and reptiles relative to species richness, IUCN status, and predicted global change. We classify the scope of available genomic resources by their potential applicability to global change. Finally, we examine global patterns of collaborations in genomic studies. Our findings underscore current priorities for expanding genomic resources, especially those aimed at predicting adaptive potential to future environmental change. Our results also highlight the need for improved global collaborations in genomic research, resource sharing, and capacity building in the Global South.

Genetic Determination of a Cryptic Species in the Littoraria Genus With Whole-Genome Molecular Resolution

Recognizing cryptic species is crucial for understanding global biodiversity. The intertidal snail Littoraria flammea is potentially a cryptic species of L. melanostoma widely distributed in the Northwest Pacific. However, the evidence from traditional morphology and single genetic markers is inconsistent. Our study combined quantitative morphological and whole-genome molecular data to clarify the phylogenetic relationship of three species (L. flammea, L. aff. melanostoma, and L. melanostoma). Three-dimensional models of shells revealed significant differences in morphology between L. flammea and L. melanostoma. Neutral SNPs indicated that individuals of L. flammea and L. melanostoma were in different clusters. The ratio of interspecific F ST to intraspecific F ST between L. flammea and L. melanostoma (16) was much larger than the lowest ratio (2.31) in six published genera with cryptic species in gastropods. Non-neutral SNPs disclosed divergence in functional genes related to reproduction and protein binding. The morphological and phylogenetic analyses corroborated the transitional status of L. aff. melanostoma. These results confirmed that the L. flammea snails north of the Yangtze River Estuary is a cryptic species of L. melanostoma, and allopatric speciation occurs in the L. melanostoma complex.

Genome-wide association analysis reveals the genetic basis of thermal tolerance in dwarf surf clam Mulinia lateralis

Recently, elevated seawater temperatures have resulted numerous adverse effects, including significant mortality among bivalves. The dwarf surf clam, Mulinia lateralis, is considered a valuable model species for bivalve research due to its rapid growth and short generation time. The successful cultivation in laboratory setting throughout its entire life cycle makes it an ideal candidate for exploring the potential mechanisms underlying bivalve responses to thermal stress. In this study, a total of 600 clams were subjected to a 17-day thermal stress experiment at a temperature of 30 °C which is the semi-lethal temperature for this species. Ninety individuals who perished initially were classified as heat-sensitive populations (HSP), while 89 individuals who survived the experiment were classified as heat-tolerant populations (HTP). Subsequently, 179 individuals were then sequenced, and 21,292 single nucleotide polymorphisms (SNPs) were genotyped for downstream analysis. The heritability estimate for survival status was found to be 0.375 ± 0.127 suggesting a genetic basis for thermal tolerance trait. Furthermore, a genome-wide association study (GWAS) identified three SNPs and 10 candidate genes associated with thermal tolerance trait in M. lateralis. These candidate genes were involved in the ETHR/EHF signaling pathway and played pivotal role in signal sensory, cell adhesion, oxidative stress, DNA damage repair, etc. Additionally, qPCR results indicated that, excluding MGAT4A, ZAN, and RFC1 genes, all others exhibited significantly higher expression in the HTP (p < 0.05), underscoring the critical involvement of the ETHR/EHF signaling pathway in M. lateralis' thermal tolerance. These results unveil the presence of standing genetic variations associated with thermal tolerance in M. lateralis, highlighting the regulatory role of the ETHR/EHF signaling pathway in the bivalve's response to thermal stress, which contribute to comprehension of the genetic basis of thermal tolerance in bivalves.

Altering traits and fates of wild populations with Mendelian DNA sequence modifying Allele Sails

Population-scale genome modification can alter the composition or fate of wild populations. Synthetic gene drives provide one set of tools, but their use is complicated by scientific, regulatory, and social issues associated with transgene persistence and flow. Here we propose an alternative approach. An Allele Sail consists of a genome editor (the Wind) that introduces DNA sequence edits, and is inherited in a Mendelian fashion. Meanwhile, the edits (the Sail) experience an arithmetic, Super-Mendelian increase in frequency. We model this system and identify contexts in which a single, low frequency release of an editor brings edits to a very high frequency. We also identify conditions in which manipulation of sex determination can bring about population suppression. In regulatory frameworks that distinguish between transgenics (GMO) and their edited non-transgenic progeny (non-GMO) Allele Sails may prove useful since the spread and persistence of the GM component can be limited.

Flight or fight: different strategies of intertidal periwinkle Littoraria sinensis coping with high temperature across populations

Intertidal organisms usually live near their upper thermal limits, and are vulnerable to future global warming. As a vital response to thermal stress, thermoregulatory strategy in physiological and behavioral performance is essential for organisms coping with thermal stress and surviving the changing world. To investigate the relationship between the thermoregulatory strategy and habitat temperature, in the present study, we comparatively investigated the thermal responsive strategy among different geographic populations of the supralittoral snail Littoraria sinensis by determining snails' cardiac function and behavioral performance. Our results indicated that populations inhabiting high ambient temperatures had higher sublethal temperatures (i.e. Arrhenius breakpoint temperatures, ABTs, the temperature at which the heart rate shapely decreases with further heating) and lethal temperatures (i.e. Flatline temperatures, FLTs, the temperature at which heart rate ceases), and behaved less actively (e.g. shorter moving distances and shorter moving time) in the face of high and rising temperatures-a physiological fight strategy. On the other hand, populations at relatively low ambient temperatures had relatively lower physiological upper thermal limits with lower ABTs and FLTs and moved more actively in the face of high and rising temperatures-a behavioral flight strategy. These results demonstrate that the thermoregulatory strategies of the snails are closely related to their habitat temperatures and are different among populations surviving divergent thermal environments.

Genome-wide sequencing reveals geographical variations in the thermal adaptation of an aquaculture species with frequent seedling introductions

Climate change and human activity are essential factors affecting marine biodiversity and aquaculture, and understanding the impacts of human activities on the genetic structure to increasing high temperatures is crucial for sustainable aquaculture and marine biodiversity conservation. As a commercially important bivalve, the Manila clam Ruditapes philippinarum is widely distributed along the coast of China, and it has been frequently introduced from Fujian Province, China, to other regions for aquaculture. In this study, we collected four populations of Manila clams from different areas to evaluate their thermal tolerance by measuring cardiac performance and genetic variations using whole-genome resequencing. The upper thermal limits of the clams showed high variations within and among populations. Different populations displayed divergent genetic compositions, and the admixed population was partly derived from the Zhangzhou population in Fujian Province, implying a complex genomic landscape under the influence of local genetic sources and human introductions. Multiple single nucleotide polymorphisms (SNPs) were associated with the cardiac functional traits, and some of these SNPs can affect the codon usage and the structural stability of the resulting protein. This study shed light on the importance of establishing long-term ecological and genetic monitoring programs at the local level to enhance resilience to future climate change.

Roles of multi-level temperature-adaptive responses and microhabitat variation in establishing distributions of intertidal species

How intertidal species survive their harsh environment and how best to evaluate and forecast range shifts in species distribution are two important and closely related questions for intertidal ecologists and global change biologists. Adaptive variation in responses of organisms to environmental change across all levels of biological organization - from behavior to molecular systems - is of key importance in setting distribution patterns, yet studies often neglect the interactions of diverse types of biological variation (e.g. differences in thermal optima owing to genetic and acclimation-induced effects) with environmental variation, notably at the scale of microhabitats. Intertidal species have to cope with extreme and frequently changing thermal stress, and have shown high variation in thermal sensitivities and adaptive responses at different levels of biological organization. Here, I review the physiological and biochemical adaptations of intertidal species to environmental temperature on multiple spatial and temporal scales. With fine-scale datasets for the thermal limits of individuals and for environmental temperature variation at the microhabitat scale, we can map the thermal sensitivity for each individual in different microhabitats, and then scale up the thermal sensitivity analysis to the population level and, finally, to the species level by incorporating physiological traits into species distribution models. These more refined mechanistic models that include consideration of physiological variations have higher predictive power than models that neglect these variations, and they will be crucial to answering the questions posed above concerning adaptive mechanisms and the roles they play in governing distribution patterns in a rapidly changing world.