Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion

Population Genetic Divergence among Worldwide Gene Pools of the Mediterranean Mussel Mytilus galloprovincialis

The Mediterranean mussel Mytilus galloprovincialis is distributed in both hemispheres either natively or introduced. The updated population genetic distribution of this species provides a useful knowledge against which future distribution shifts could be assessed. This study, performed with seven microsatellite markers and three reference species (M. edulis, M. chilensis and M. trossulus), aimed to determine the scenario of genetic divergence between 15 samples of M. galloprovincialis from 10 localities in Europe, Africa, Asia, Australia, North America and South America. In agreement with previous data, M. trossulus was the most divergent taxon of the genus, but M. chilensis appeared as an intermediate taxon between M. edulis and M. galloprovincialis, though closer to this latter. M. galloprovincialis from the Atlantic Northeast appears as the most likely source of worldwide exotic settlements instead of the previously thought Mediterranean population. The successful worldwide establishment of M. galloprovincialis suggests it is a flexible evolutionary species (FES), i.e., a species or population whose genetic background allows it to rapidly adapt to changing environments. This natural endowed plastic adaptation makes it a candidate resilient species amidst the ongoing climatic change.

Cryptic Species in Ecotoxicology

The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Rhythms and Clocks in Marine Organisms

The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.

Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization

Human-mediated pressures, including bioinvasions, threaten the biotas of every continent. Hybridization and introgression between invasive and native species may result in loss of genetic integrity of native taxa but, in many cases, these events are hard to detect because the invader is impossible to tell apart from the native taxon. The problem of cryptic invasive taxa and its importance for biodiversity protection have been underestimated, because of the limited number of studies of broadly distributed taxa using sensitive nuclear DNA markers. We employed a panel of 51 single nucleotide polymorphism (SNP) markers to examine genetic interactions between Australian native smooth-shelled mussels, Mytilus planulatus, and invasive and cryptic Northern Hemisphere M. galloprovincialis along 4400 km of coastline from the Pacific to the Indian Ocean. Overall, 20.8% of mussels from ten sites were native species. The centre of distribution of M. planulatus is in south-eastern Australia, in particular in Tasmania. We suggest that ongoing spatial and temporal monitoring of Tasmanian sites is required to test for the presence of M. galloprovincialis and its possible further spread, and that hatchery production of M. planulatus for farming and reseeding into the wild may help reduce the likelihood of its loss.

Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation

Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.

Development and Validation of a Multi-Locus PCR-HRM Method for Species Identification in Mytilus Genus with Food Authenticity Purposes

DNA-based methods using informative markers such as single nucleotide polymorphism (SNPs) are suitable for reliable species identification (SI) needed to enforce compliance with seafood labelling regulations (EU No.1379/2013). We developed a panel of 10 highly informative SNPs to be genotyped by PCR-High resolution melting (HRM) for SI in the Mytilus genus through in silico and in vitro stages. Its fitness for purpose and concordance were assessed by an internal validation process and by the transference to a second laboratory. The method was applicable to identify M. chilensis, M. edulis, M. galloprovincialis and M. trossulus mussels, fresh, frozen and canned with brine, oil and scallop sauce, but not in preserves containing acetic acid (wine vinegar) and tomato sauce. False-positive and negative rates were zero. Sensitivity, expressed as limit of detection (LOD), ranged between 5 and 8 ng/μL. The method was robust against small variations in DNA quality, annealing time and temperature, primer concentration, reaction volume and HRM kit. Reference materials and 220 samples were tested in an inter-laboratory assay obtaining an “almost perfect agreement” (κ = 0.925, p < 0.001). In conclusion, the method was suitable for the intended use and to be applied in the seafood industry.

Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

Anthropogenic hybridization at sea: three evolutionary questions relevant to invasive species management

Species introductions promote secondary contacts between taxa with long histories of allopatric divergence. Anthropogenic contact zones thus offer valuable contrasts to speciation studies in natural systems where past spatial isolations may have been brief or intermittent. Investigations of anthropogenic hybridization are rare for marine animals, which have high fecundity and high dispersal ability, characteristics that contrast to most terrestrial animals. Genomic studies indicate that gene flow can still occur after millions of years of divergence, as illustrated by invasive mussels and tunicates. In this context, we highlight three issues: (i) the effects of high propagule pressure and demographic asymmetries on introgression directionality, (ii) the role of hybridization in preventing introduced species spread, and (iii) the importance of postzygotic barriers in maintaining reproductive isolation. Anthropogenic contact zones offer evolutionary biologists unprecedented large scale hybridization experiments. In addition to breaking the highly effective reproductive isolating barrier of spatial segregation, they allow researchers to explore unusual demographic contexts with strong asymmetries. The outcomes are diverse, from introgression swamping to strong barriers to gene flow, and lead to local containment or widespread invasion. These outcomes should not be neglected in management policies of marine invasive species. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Trans-Atlantic Distribution and Introgression as Inferred from Single Nucleotide Polymorphism: Mussels Mytilus and Environmental Factors

Large-scale climate changes influence the geographic distribution of biodiversity. Many taxa have been reported to extend or reduce their geographic range, move poleward or displace other species. However, for closely related species that can hybridize in the natural environment, displacement is not the only effect of changes of environmental variables. Another option is subtler, hidden expansion, which can be found using genetic methods only. The marine blue mussels Mytilus are known to change their geographic distribution despite being sessile animals. In addition to natural dissemination at larval phase—enhanced by intentional or accidental introductions and rafting—they can spread through hybridization and introgression with local congeners, which can create mixed populations sustaining in environmental conditions that are marginal for pure taxa. The Mytilus species have a wide distribution in coastal regions of the Northern and Southern Hemisphere. In this study, we investigated the inter-regional genetic differentiation of the Mytilus species complex at 53 locations in the North Atlantic and adjacent Arctic waters and linked this genetic variability to key local environmental drivers. Of seventy-nine candidate single nucleotide polymorphisms (SNPs), all samples were successfully genotyped with a subset of 54 SNPs. There was a clear interregional separation of Mytilus species. However, all three Mytilus species hybridized in the contact area and created hybrid zones with mixed populations. Boosted regression trees (BRT) models showed that inter-regional variability was important in many allele models but did not prevail over variability in local environmental factors. Local environmental variables described over 40% of variability in about 30% of the allele frequencies of Mytilus spp. For the 30% of alleles, variability in their frequencies was only weakly coupled with local environmental conditions. For most studied alleles the linkages between environmental drivers and the genetic variability of Mytilus spp. were random in respect to “coding” and “non-coding” regions. An analysis of the subset of data involving functional genes only showed that two SNPs at Hsp70 and ATPase genes correlated with environmental variables. Total predictive ability of the highest performing models (r² between 0.550 and 0.801) were for alleles that discriminated most effectively M. trossulus from M. edulis and M. galloprovincialis, whereas the best performing allele model (BM101A) did the best at discriminating M. galloprovincialis from M. edulis and M. trossulus. Among the local environmental variables, salinity, water temperature, ice cover and chlorophyll a concentration were by far the greatest predictors, but their predictive performance varied among different allele models. In most cases changes in the allele frequencies along these environmental gradients were abrupt and occurred at a very narrow range of environmental variables. In general, regions of change in allele frequencies for M. trossulus occurred at 8–11 psu, 0–10 °C, 60%–70% of ice cover and 0–2 mg m⁻³ of chlorophyll a, M. edulis at 8–11 and 30–35 psu, 10–14 °C and 60%–70% of ice cover and for M. galloprovincialis at 30–35 psu, 14–20 °C.

Replicated anthropogenic hybridisations reveal parallel patterns of admixture in marine mussels

Human-mediated transport creates secondary contacts between genetically differentiated lineages, bringing new opportunities for gene exchange. When similar introductions occur in different places, they provide informally replicated experiments for studying hybridisation. We here examined 4,279 Mytilus mussels, sampled in Europe and genotyped with 77 ancestry-informative markers. We identified a type of introduced mussels, called "dock mussels," associated with port habitats and displaying a particular genetic signal of admixture between M. edulis and the Mediterranean lineage of M. galloprovincialis. These mussels exhibit similarities in their ancestry compositions, regardless of the local native genetic backgrounds and the distance separating colonised ports. We observed fine-scale genetic shifts at the port entrance, at scales below natural dispersal distance. Such sharp clines do not fit with migration-selection tension zone models, and instead suggest habitat choice and early-stage adaptation to the port environment, possibly coupled with connectivity barriers. Variations in the spread and admixture patterns of dock mussels seem to be influenced by the local native genetic backgrounds encountered. We next examined departures from the average admixture rate at different loci, and compared human-mediated admixture events, to naturally admixed populations and experimental crosses. When the same M. galloprovincialis background was involved, positive correlations in the departures of loci across locations were found; but when different backgrounds were involved, no or negative correlations were observed. While some observed positive correlations might be best explained by a shared history and saltatory colonisation, others are likely produced by parallel selective events. Altogether, genome-wide effect of admixture seems repeatable and more dependent on genetic background than environmental context. Our results pave the way towards further genomic analyses of admixture, and monitoring of the spread of dock mussels both at large and at fine spacial scales.

Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.