Location-Dependent DNA Methylation Signatures in a Clonal Invasive Crayfish

DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental parameters have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of context-dependent DNA methylation signatures in a clonal animal.

Divergent temperature-specific metabolic and feeding rates of native and invasive crayfish

Temperature is one of the most important factors governing the activity of ectothermic species, and it plays an important but less studied role in the manifestation of invasive species impacts. In this study, we investigated temperature-specific feeding and metabolic rates of invasive and native crayfish, and evaluated how temperature regulates their ecological impacts at present and in future according to different climatic scenarios by bioenergetics modelling. We conducted a series of maximum food consumption experiments and measured the metabolic rates of cold-adapted native noble crayfish (Astacus astacus) and invasive signal crayfish (Pacifastacus leniusculus) originally from a warmer environment over a temperature gradient resembling natural temperatures in Finland. The maximum feeding rates and routine metabolic rates (RMR) of native noble crayfish were significantly higher at low temperatures (< 10 °C than the rates of invasive signal crayfish. The RMRs of the species crossed at 18 °C, and the RMRs of signal crayfish were higher at temperatures above 18 °C. These findings indicate that the invader’s thermal niche has remained stable, and the potential impacts per capita are lower at suboptimal cold temperatures than for the native species. Our bioenergetics modelling showed that the direct annual predation impact of noble and signal crayfish seem similar, although the seasonal dynamics of the predation differs considerably between species. Our results highlight that the temperature-specific metabolic and feeding rates of species need to be taken into account in the impact assessment instead of simple generalisations of the direction or magnitude of impacts.

Parasite DNA detection in water samples enhances crayfish plague monitoring in asymptomatic invasive populations

Invasive species can facilitate the spread of pathogens by first providing asymptomatic host reservoirs, and then driving disease outbreaks in native populations through pathogen spillover. An example of this are invasive crayfish species in Europe (Faxonius limosus, Pacifastacus leniusculus, Procambarus clarkii), which carry the deadly plague agent (Aphanomyces astaci). Effective disease management requires comprehensive monitoring, however, pathogen detection in carrier populations with low pathogen prevalence and intensities is challenging. We simultaneously collected and analysed crayfish tissue samples of invasive crayfish populations and water samples to compare A. astaci detection in different sample types using quantitative PCR. Combined, the two sampling methods revealed A. astaci presence with DNA concentrations above limit of detection (LOD; the lowest concentration which can be detected with reasonable certainty) in 13 of 23 invasive crayfish populations. In four additional sites, A. astaci DNA concentrations below LOD were found in water. In four populations only were A. astaci concentrations above LOD detected in both sample types and in three populations in concentrations above LOD in tissue but below LOD in water. The likely reason for these discrepancies is the low A. astaci prevalence and concentration in resistant invasive crayfish, which limit detection reliability. Consistency may be improved by timing surveys with seasonal periods of high A. astaci abundance and by increasing water sampling effort. Considering the ease of collecting eDNA samples, compared to crayfish tissue sampling, eDNA methods would facilitate frequent and comprehensive surveys. However, remaining uncertainties in eDNA-based detection reveal the relevance of combining monitoring tools to improve detection of invasive pathogens and their management.

Genetic diversity of redclaw crayfish Cherax quadricarinatus von Martens 1868 using 16S mitochondrial DNA marker

There have been reported around 11 aquatic invasive alien species (IAS) found in Malaysian waters. Cherax quadricarinatus, or commonly known as Australian redclaw crayfish, is one of the invasive species. C. quadricarinatus has the potential of causing negative impacts ecologically and economically in the local environment as it has reported in several countries if they get established and not monitored properly. Habitat alteration, native species depletion and spreading of diseases are among the reported negative impacts of C. quadricarinatus. This study was conducted with the aim to assess the genetic diversity of C. quadricarinatus from 4 different populations. Uncovering the diversity and population structure of the redclaw crayfish will help in enhancing the understanding of adaptation and survival of C. quadricarinatus. Thus, the information can be used in monitoring and management of this invasive crayfish in future. DNA of C. quadricarinatus was successfully extracted from its tissue and amplified via polymerase chain reaction (PCR) using mitochondrial DNA (mtDNA) 16S gene then proceeded for sequencing and analysed using several genetic analysis software to understand the diversity, phylogeny and population structure of this invasive crayfish species. A total of 493 bp fragments of 32 samples from four sampling sites were obtained. Four haplotypes were observed which Hap-1 was the most common haplotype. The highest genetic variation is Selangor (Pi = 0.00248, Hd = 0.694). However, low levels of both haplotype and nucleotide diversity indicates the loss of genetic diversity. Analysis of molecular variance (AMOVA) results revealed that the percentage of genetic variation within the population was 69.58% while among populations was 30.42%, indicating significant genetic differentiation among population (P < 0.05). The maximum likelihood tree showed that all haplotypes were clustered and grouped together with United States, Czech Republic, China and Australia.