Genomic adaptive potential to cold environments in the invasive red swamp crayfish

Changes in Muscle Quality and Gut Microbiota of Whiteleg Shrimp (Penaeus vannamei) Within a Live Supply Chain

During farm-to-consumer transport, a live supply chain can aid in maintaining the quality of whiteleg shrimp (Penaeus vannamei). However, the changes in muscle quality and gut microbiota of shrimp in the live supply chain and their interactions are poorly understood. Here, we investigated the dynamics of cumulative survival, muscle quality, and gut microbiota in the key phases of the live shrimp supply chain: post-harvest, post-transport, post-respite, and simulated sales [ambient temperature (AT; 29 °C ± 0.3 °C); low temperature (LT; 23 °C ± 0.3 °C)]. The results suggest that among the various stages, the highest mortality (12%) occurred after transport, while the respite process was associated with enhanced gut-mediated stress resilience. Notably, the transport, 24 h sales, and 40 h sales stages were identified as three potential critical control points. Furthermore, the LT group exhibited an 8% higher survival rate, better quality parameters (34.9% higher hardness), increased abundance of Bacteroidetes (from 3.63% to 7.39%), and a reduced F: B ratio. Correlation analysis identified Xanthomonadales and Oscillospirales as potential biomarkers for maintaining quality, positively linked to survival, muscle hardness, and brightness. Our findings provide valuable insights into optimizing control strategies and microbial biomarkers for enhancing muscle quality in live supply chains and aquaculture.

A Breeding System Derived From Asexual Queen Succession in Termite Colonies From Cold Climate Regions

In social insects, geographic variation is often accompanied not only by physiological changes but also by changes in their social system. In the subterranean termite Reticulitermes speratus that exhibits a sophisticated social system, colonies in subtropical and temperate areas are founded by a pair of primary king and queen derived from sexually produced alates. Some years after colony establishment, many neotenic queens are produced parthenogenetically, which is known as asexual queen succession (AQS). This strategy boosts reproduction without inbreeding. Here we show that subarctic populations of R. speratus, where colonies founded by alates cannot be sustained due to the cold conditions, undergo inbreeding rather than AQS, with colonies headed by numerous neotenic reproductives. Genetic analysis found that most neotenic queens were produced sexually in the subarctic populations, rather than asexually. Rearing experiments using colonies consisting only of nymphs (reproductive-destined individuals) and workers revealed that more nymphs successfully established as neotenic reproductives in the subarctic populations than in temperate populations, and that a higher number of individuals were maintained in the subarctic populations. These results suggest that sexually produced nymphs in subarctic populations are highly predisposed to develop into neotenic reproductives, whereas in temperate populations, their developmental potential is predominantly directed towards becoming alates. This study demonstrates that R. speratus has adjusted to colder climatic zones by changing its sophisticated AQS reproductive system into a secondary strategy to maintain colonies, elucidating the flexible adaptation and acclimation of reproductive systems in social insects.

(Limited) Predictability of thermal adaptation in invertebrates

Evolutionary genomic approaches provide powerful tools to understand variation in and evolution of physiological processes. Untargeted genomic or transcriptomic screens can identify functionally annotated candidate genes linked to specific physiological processes, in turn suggesting evolutionary roles for these processes. Such studies often aim to inform modeling of the potential of natural populations to adapt to climate change, but these models are most accurate when evolutionary responses are repeatable, and thus predictable. Here, we synthesize the evolutionary genetic and comparative transcriptomic literature on terrestrial and marine invertebrates to assess whether evolutionary responses to temperature are repeatable within populations, across populations and across species. There is compelling evidence for repeatability, sometimes even across species. However, responses to laboratory selection and geographic variation across thermal gradients appear to be highly idiosyncratic. We also survey whether genetic/transcriptomic studies repeatedly identify candidate genes in three functional groups previously associated with the response to thermal stress: heat shock protein (Hsp) genes, proteolysis genes and immunity genes. Multiple studies across terrestrial and marine species identify candidates included in these gene sets. Yet, each of the gene sets are identified in only a minority of studies. Together, these patterns suggest that there is limited predictability of evolutionary responses to natural selection, including across studies within species. We discuss specific patterns for the candidate gene sets, implications for predictive modeling, and other potential applications of evolutionary genetics in elucidating physiology and gene function. Finally, we discuss limitations of inferences from available evolutionary genetic studies and directions for future research.

Impact of Cold Stress on Hepatopancreas Transcriptomic and Metabolomic in Red Swamp Crayfish Procambarus clarkii

The aquaculture industry of red swamp crayfish (RSC), Procambarus clarkii, has grown significantly in recent decades due to increasing market demand. In China, low water temperatures, particularly during overwintering, pose a challenge, hindering the development of the RSC aquaculture industry in northern regions. Understanding the molecular mechanism of RSCs' responses to cold stress could be beneficial for its aquaculture practices. In this study, we exposed RSCs to 4 °C (T4) and 22 °C (T22: control) for 96 h. Transcriptomic and metabolomic analyses of hepatopancreas tissues were performed to identify key genes and metabolites that participate in cold stress response. A total of 787 differentially expressed genes (DEGs) and 198 differentially expressed metabolites (DEMs) were identified between T4 and T22. DEGs were significantly enriched in KEGG pathways related to carbohydrate, lipid, amino acid, and nucleotide metabolism, immunity, and signaling, while DEMs were significantly enriched in pathways associated with lipid and amino acid metabolism and membrane transport. The results indicated that cold stress altered RSCs' metabolism and their innate immune system. This study provides valuable information to increase our understanding of cold stress responses in RSCs.

Genetic Mechanism Analysis Related to Cold Tolerance of Red Swamp Crayfish, Procambarus clarkii

In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise FST values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.

Some Like It Cold: Long-Term Assessment of a Near-Global Invader

Long-term studies depicting the multicontinental invasion trajectories of species are often constrained by the scarcity of documented records, especially for invertebrates. The red swamp crayfish, Procambarus clarkii (Decapoda: Cambaridae), stands out as an uncommon example of hypersuccessful invasive species with a well-known invasion history at both regional and global levels. This allows for the use of its records to track distribution dynamics and bioclimatic preferences over time. Through multiple temporal comparisons, the global bioclimatic tendencies of the species have been explored over a period exceeding a century (1854-2023) using linear models with generalized least squares estimation and two-sample t-tests. This specific setup provides a rare focus on biological invasions at both broad temporal and spatial scales. The results highlight climatic trends in the invasion process of the species, including decreases in the values of bioclimatic variables associated with temperature and precipitation. This trend encompasses not only mean values but also both extreme (minimum and maximum) and is coupled with increases in elevation and aridity values in the areas with the presence of the species. The findings indicate that the species can engage in new ecological interactions and further affect range-restricted species in climatic refuges once considered protected. These findings help anticipate changes in the species' invasion trajectory, suggesting possible expansions into colder, less humid climates and higher altitudes. This knowledge supports effective monitoring and early detection for management and conservation efforts.

Insights from the past: Invasion trajectory and niche trends of a global freshwater invader

Freshwater ecosystems are invaded by a non-random selection of taxa, among which crayfish stand out with successful examples worldwide. Species distribution models (SDMs) have been used to detect suitable areas for invasive species and predict their potential distributions. However, these prediction exercises assume the stability of realized environmental niches, which is uncertain during invasion. Worldwide evaluations involving cosmopolitan invaders may be particularly useful but have seldom been considered. Focusing on the successful invasion history of the red swamp crayfish, Procambarus clarkii, we assessed its geographic expansion and niche trends over time. Based on global occurrences from 1854 to 2022, multiple sequential SDMs have been implemented based on a set of bioclimatic variables. The environmental suitability for each period was projected through to the next period(s) using an ensemble procedure of commonly used SDM algorithms. As the records of the species are known, it was possible to check whether the modelling projections were concordant with the observed expansion of red swamp crayfish at a global scale. This also permitted analysis of its realized niche, and its dynamics, during different expansion phases. SDM maps based on past species records showed concordance with the known crayfish distributions and yielded similar spatial patterns with outputs overperforming random combinations of cells in term of suitability. The results also reflect the stability of the species niche, which despite some expansions during the invasion process, changed little in terms of main position in functional space over time. SDMs developed in the early stages of invasion provide useful insights but also tend to underpredict the potential range compared to models that were built for later stages. Our approach can be easily transferable to other well-documented taxa and represents valuable evidence for validating the use of SDMs, considering a highly dynamic world where biogeographical barriers are often bypassed.

Niche dynamics along two centuries of multiple crayfish invasions

The realised ecological niches of species may change in response to dynamic abiotic and biotic environments, particularly under fast global change. To fully understand the dynamics of niche features and their drivers, it is essential to have a long-term view of species distributions and the factors that may have influenced them. Here, we analysed the distribution and niche dynamics of the Italian crayfish (Austropotamobius fulcisianus) in the Iberian Peninsula over the past 200 years. The Italian crayfish was introduced to Spain in the 16th century, and spread due to multiple stocking events until the 1970s, when two North American crayfish (red swamp crayfish Procambarus clarkii, and signal crayfish Pacifastacus leniusculus) were introduced. Both North American species are carriers of a pathogen (Aphanomyces astaci, the causal agent of crayfish plague) lethal to the Italian crayfish. We hypothesised that the realised niche of the Italian crayfish, both in breadth and in position, has changed over time following changes in its range. The distribution of the Italian crayfish expanded from the mid-19th century until the mid-20th century, in association with an enlargement of its realised niched, mostly towards less abrupt and more coastal-influenced areas. After the introduction of the North American crayfishes, the collapse of the Italian crayfish involved a niche shift towards rough terrains in mountain areas. North American crayfish have eventually occupied most of the Italian crayfish's niche space, with the few no-coexistence areas being relegated to the most abrupt and high-elevation territories. Our historical approach allowed us to document and understand the highly dynamic distribution and niche of the Italian crayfish in the presence of invader counterparts, and to explore the environmental conditions under which their coexistence is minimised.