Kinetics of metal and metalloid concentrations in holopelagic Sargassum reaching coastal environments.

Since 2011, the Caribbean Islands have experienced unprecedented stranding of a pelagic brown macroalgae Sargassum inducing damages for coastal ecosystems and economy. This study measures the kinetics of metal trace elements (MTE) in Sargassum reaching different coastal environments. In July 2021, over a period of 25 days, fixed experimental floating cages containing the three Sargassum morphotypes (S. fluitans III and S. natans I and VIII) were placed in three different coastal habitats (coral reef, seagrass, and mangrove) in Guadeloupe (French West Indies). Evolution of biomasses and their total phenolic content of Sargassum reveals that environmental conditions of caging were stressful and end up to the death of algae. Concentrations of 19 metal(loid) trace elements were analyzed and three shapes of kinetics were identified with the MTE that either concentrate, depurate, or remains stable. In the mangrove, evolution of MTE was more rapid than the two other habitats a decrease of the As between 70 and 50 µg g-1 in the mangrove. Sargassum natans I presented a different metal composition than the two other morphotypes, with higher contents of As and Zn. All Sargassum morphotype are rapidly releasing the metal(oid)s arsenic (As) when they arrive in studied coastal habitats. In order to avoid the transfer of As from Sargassum to coastal environments, Sargassum stranding should be avoided and their valorization must take into account their As contents.

Temporal variations in fecal indicator bacteria in bathing water and sediment in a coastal ecosystem (Aytré Bay, Charente-Maritime, France).

This study presents the fecal contamination dynamic at the two bathing sites of Aytré Bay (Charente Maritime, France). We quantified fecal indicator bacteria (FIB) abundances (Escherichia coli and enterococci) from water and sediment samples over one-year survey. Then we measured biological (bacterial abundance, chlorophyll-a), physico-chemical (dissolved nutrients and oxygen, salinity, pH …) and climatic (temperatures, rainfall and tidal coefficient) parameters. Results showed that FIB abundances were occasionally higher than the European regulatory threshold during winter, summer and fall. The "poor quality" of the bathing water was due to high enterococci abundance. We found negative significant correlations between FIB and water temperature and salinity, and positive significant correlations between FIB and rainfall, PO4, NO3, NO2, and SiO2 mainly in water. Relationships between parameters showed that during summer and spring the main environmental drivers were temperature and salinity, while in fall and winter they were rainfall and dissolved nutrients.

Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins.

Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.

SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms.

Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.

Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator.

Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.

Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic.

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans.

Restriction-site-associated DNA tag (RAD-tag) sequencing has become a popular approach to generate thousands of SNPs used to address diverse questions in population genomics. Comparatively, the suitability of RAD-tag genotyping to address evolutionary questions across divergent species has been the subject of only a few recent studies. Here, we evaluate the applicability of this approach to conduct genome-wide scans for polymorphisms across two cetacean species belonging to distinct families: the short-beaked common dolphin (Delphinus delphis; n = 5 individuals) and the harbour porpoise (Phocoena phocoena; n = 1 individual). Additionally, we explore the effects of varying two parameters in the Stacks analysis pipeline on the number of loci and level of divergence obtained. We observed a 34% drop in the total number of loci that were present in all individuals when analysing individuals from the distinct families compared with analyses restricted to intraspecific comparisons (i.e. within D. delphis). Despite relatively stringent quality filters, 3595 polymorphic loci were retrieved from our interfamilial comparison. Cetaceans have undergone rapid diversification, and the estimated divergence time between the two families is relatively recent (14-19 Ma). Thus, our results showed that, for this level of divergence, a large number of orthologous loci can still be genotyped using this approach, which is on par with two recent in silico studies. Our findings constitute one of the first empirical investigations using RAD-tag sequencing at this level of divergence and highlights the great potential of this approach in comparative studies and to address evolutionary questions.

marmap: A package for importing, plotting and analyzing bathymetric and topographic data in R.

In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

Variability of fresh- and salt-water marshes characteristics on the west coast of France: a spatio-temporal assessment.

The degradation of water quality and the multiple conflicts of interest between users make marsh restoration very important. A Water Quality Evaluation System (WQES) was developed for river systems by the European Water Framework Directive (WFD). Some form of biologically-based, habitat-specific reference standard seems absolutely essential for wise management and stewardship of marsh ecosystems. The goal of this study was to develop a statistical method to define and to characterize a water body typology for drained marshes of the Charente-Maritime wetlands on the French Atlantic coast, placing particular emphasis on environmental factors as hydraulic functioning, human activities and pedological substratum. The Charente-Maritime marshes represent a good field study because of his high diversity of types of marshes and of anthropogenic activities in a restrictive area thus erasing spatial climatic effect (latitude effect). The statistical method developed here had permitted to define and characterize 12 different water bodies, 7 in freshwater (F1 to F7) and 5 in salt water marshes for the Charente-Maritime area. This typology demonstrated an important link between the size catchment area, nitrate concentrations, and leaching of precipitation from cultured soils. Even though the Charente-Maritime marshes are strongly impacted by humans, they may still retain the ability to remove nitrate. The increasing gradient of water renewal in the freshwater marshes from F1 to F7 explained the decreasing gradient of eutrophication. A better management of the hydrodynamic of the marshes can avoid eutrophication risk on the coastal sea area. Reliance on the WFD parameter set necessarily placed limits on the kinds of interpretations that could be made and on the study's potential contribution to the basic science of marshes. Ecologically-based insights regarding both external flows (links between ecosystems, meta-ecosystem theory) and internal flows (structure of the planktonic food web) seem an essential prerequisite for further advances in the study of marsh ecosystems.

An evaluation of teeth of ringed seals (Phoca hispida) from Greenland as a matrix to monitor spatial and temporal trends of mercury and stable isotopes.

Total mercury (Hg) concentrations were measured in teeth of ringed seals from Qeqertarsuaq, central West Greenland (1982 to 2006) and Ittoqqortoormiit, central East Greenland (1986 to 2006). Stable isotopic ratios of carbon ((13)C/(12)C) and nitrogen ((15)N/(14)N) were determined as well to provide insights into diet variations between regions or through time. Mercury concentrations decreased the first years of life of the animals suggesting that Hg had been transferred from the mother to the foetus and newborn. The Hg concentrations in teeth were significantly lesser in ringed seals from central West Greenland compared to those from central East Greenland. Carbon and nitrogen stable isotopic values measured in the animals differed also significantly between the two regions. Increasing temporal trends of dental Hg concentrations between 1994 and 2006 were observed in ringed seals from both central West Greenland and central East Greenland. These increases were attributed to global changes in environmental Hg levels since no temporal trends in delta(15)N values were found to support the hypothesis of a diet shift over time. Furthermore, a decreasing temporal trend in delta(13)C values was observed in the teeth of seals from central East Greenland, and explained by a likely change over time towards more pelagic feeding habits; alternatively, the so-known Seuss effect was thought to be responsible for this decrease. Finally, it was concluded that the tooth of ringed seal was a good monitoring tissue to assess Hg trends.