Cristina Di Muri

Italian National Research Council | CNR · Research Institute on Terrestrial Ecosystems (IRET)

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies...

Background Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non‐invasive biodiversity monitoring. Aims In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of fish communities in two aquaculture ponds and to evaluate the detection sensitivity of this tool for low‐density species alongsi...

Efficient DNA extraction is fundamental to molecular studies. However, commercial kits are expensive when a large number of samples need to be processed. Here we present a simple, modular and adaptable DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types (modular universal DNA extraction method or Mu-DNA). We com...

Freshwater biodiversity is critically affected by human modifications of terrestrial land use and land cover (LULC). Yet, knowledge of the spatial extent and magnitude of LULC-aquatic biodiversity linkages is still surprisingly limited, impeding the implementation of optimal management strategies. Here, we compiled fish diversity data across a 160,...

Simple Summary An in-depth study of the feeding habits characterizing bioinvaders may provide key information on the magnitude of their impacts on recipient communities. Specifically, if invaders’ trophic niche is superimposed on that of native species, interspecific competition may increase, resulting in negative consequences for the competing spe...

Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring in aquatic environments where the method has repeatedly shown comparable or better performance than conventional approaches to fish monitoring. This method has been developed and deployed, primarily using shoreline sampling during the winter months, across 101 lakes in G...

LifeWatch ERIC, the e-Science European infrastructure for biodiversity and ecosystem research, launched an Internal Joint Initiative on Non-indigenous Species and Invasive Alien Species (NIS-IAS) as they are considered one of the major drivers of biodiversity and ecosystem change. Here, the case study focused on the trophic biogeography of invasive...

There is a growing recognition that an advanced understanding of the trophic characteristics of an invasive consumer can provide important information on its ecological impact. In recent years, the blue swimming crab Portunus segnis, one of the earliest Lessepsian invaders, has considerably expanded its distribution range in the Mediterranean Sea,...

Background Freshwater ecosystems are amongst the most threatened habitats on Earth; nevertheless, they support about 9.5% of the known global biodiversity while covering less than 1% of the globe’s surface. A number of anthropogenic pressures are impacting species diversity in inland waters and, amongst them, the spread of invasive alien species is...

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish p...

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish p...

The characterisation of functional traits of non-indigenous and invasive species is crucial to assess their impact within invaded habitats. Successful biological invasions are often facilitated by the generalist diet of the invaders which can modify their trophic position and adapt to new ecosystems determining changes in their structure and functi...

Biomonitoring of complex heterogeneous environments is highly challenging. Fish in deep water bodies occupy different habitats, so a combination of survey methods has traditionally been used. Environmental DNA (eDNA) metabarcoding is a novel monitoring tool that can overcome spatial heterogeneity in a highly sensitive and entirely non-invasive mann...

Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site...

Tropical and subtropical freshwater habitats are among the most biodiverse ecosystems worldwide, containing a characteristic fauna and high numbers of endemic species. However, exploitation of organisms, global climate change, pollution and the introduction of invasive species are severely threatening this diversity. Implementation of appropriate c...

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understo...

Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spa...

Mu-DNA is designed to be a simple and modular spin column-based DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types. Here we presentoptimised Mu-DNA protocols for soil, tissue and water samples. Each protocol consists of five stages for DNA extraction: lysis, inhibitor removal, silica binding, wash and elution....

Mu-DNA is designed to be a simple and modular spin column-based DNA extraction ‘toolkit’ for the isolation of high purity DNA from multiple sample types. Here we presentoptimised Mu-DNA protocols for soil, tissue and water samples. Each protocol consists of five stages for DNA extraction: lysis, inhibitor removal, silica binding, wash and elution....

Out of nearly 30,000 teleosts dwelling in our planet's water bodies, only hundreds of them are commercially exploited and prevail on the global food market. Yet, our estimates of the species actually underpinning global trade is severely hampered by inaccuracy and non-compliance in labelling and reporting. Here, we target ethnic food stores in two...

Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as 'redfish', but little is known about the number,...

Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70%) of fish species substitution. Based on indications that the European seafood retail...

Detailed overview of the sample identification using both Genbank and the different BOLD reference databases Samples of Seabass are not included as identification was only possible with GenBank and is presented in Table 1. Samples marked with an astrics are the samples for which detailed species names were given from the waiting staff, however this...

Raw Data Sample names, genbank accession numbers and the sequences

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths fr...

Describe the outliers`detection methods in details and provide results for these tests. (DOCX)

Molecular markers information. Microsatellite loci primer sequences, reference genome and authors. (DOCX)

Results from the LnRH method [45] to detect outlier loci. (DOCX)

Graphical plot of mean Ln[P(K)] from STRUCTURE [56, 57] simulation. (DOCX)

Historical collection, specimens and data collection. (DOCX)

Locus-by-locus Probability of Identity (PID) and Probability of Identity of Siblings (PID(sib)) estimations [36]. (DOCX)

Summary of genetic diversity observed at 7 microsatellite loci from the sampled archived materials. (DOCX)

FST values and significances from the fdist [43] outlier detection test. (DOCX)