Acoustic fish community in the Madeira Archipelago (North Atlantic Ocean): Characterization of sound diversity and daily patterns.

Marine ecosystems are increasingly subjected to anthropogenic pressures, which demands urgent monitoring plans. Understanding soundscapes can offer unique insights into the ocean status providing important information and revealing different sounds and their sources. Fishes can be prominent soundscape contributors, making passive acoustic monitoring (PAM) a potential tool to detect the presence of vocal fish species and to monitor changes in biodiversity. The major goal of this research was to provide a first reference of the marine soundscapes of the Madeira Archipelago focusing on fish sounds, as a basis for a long-term PAM program. Based on the literature, 102 potentially vocal and 35 vocal fish species were identified. Additionally 43 putative fish sound types were detected in audio recordings from two marine protected areas (MPAs) in the Archipelago: the Garajau MPA and the Desertas MPA. The Garajau MPA exhibited higher fish vocal activity, a greater variety of putative fish sound types and higher fish sound diversity. Lower abundance of sounds was found at night at both MPAs. Acoustic activity revealed a clear distinction between diurnal and nocturnal fish groups and demonstrated daily patterns of fish sound activity, suggesting temporal and spectral partitioning of the acoustic space. Pomacentridae species were proposed as candidates for some of the dominant sound types detected during the day, while scorpionfishes (Scorpaena spp.) were proposed as sources for some of the dominant nocturnal fish sounds. This study provides an important baseline about this community acoustic behaviour and is a valuable steppingstone for future non-invasive and cost-effective monitoring programs in Madeira.

Do catadromous thinlip grey mullet benefit from shifting to freshwater? A perspective from fatty acid signature analysis.

To investigate the potential benefits of the catadromous thinlip grey mullet (Chelon ramada Risso, 1827) migration to freshwater, the total lipid content and fatty acid (FA) profile of female's muscle and gonads caught in both the estuary and river were analyzed. The freshwater contingent presented a higher body condition, greater muscle gross energy, and larger gonads with higher lipid reserves. These animals showed a muscle profile rich in C16:1n-7 and lower LC-PUFA that contrast with the higher relative amount of C18:1n-9, n-3 FA, and unsaturated LC-PUFA, such as C18 and C20 FA found in the estuarine contingent. The gonads of both contingents showed a constant and high relative amount of polyunsaturated FAs (PUFA, 37%). However, in terms of essential fatty acids (EFAs), the estuarine contingent had a higher relative amount of C18:2n-6, C20:4n-6, C20:5n-3, and C22:6n-3. On the other hand, the freshwater contingent showed a higher relative amount of n-3 FA precursors, namely C18:3n-3, and a still low relative amount of C22:6n-3. This suggests a mismatch between the metabolic omega-3 pathway and the physiological maturity stages, similar to a phenomenon of dormancy. In this sense, not all these individuals may reproduce annually, and the later stages of gonad development will require supplementary energy derived from feeding at the estuary. Thus, freshwater migration may promote a reproductive strategy enabling adults to take advantage of the warm and food-rich summer/autumn period, adjust spawning and juvenile appearance, and reduce the population's exposure to habitat changes and/or stochastic events.

Seascape genomics reveals limited dispersal and suggests spatially varying selection among European populations of sea lamprey (Petromyzon marinus).

Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviors. Despite being a freshwater, free-living organism for a large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lamprey's genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing of 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30,910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the North Eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species' dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with the abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites.

The Biological Assessment and Rehabilitation of the World's Rivers: An Overview.

The biological assessment of rivers i.e., their assessment through use of aquatic assemblages, integrates the effects of multiple-stressors on these systems over time and is essential to evaluate ecosystem condition and establish recovery measures. It has been undertaken in many countries since the 1990s, but not globally. And where national or multi-national monitoring networks have gathered large amounts of data, the poor water body classifications have not necessarily resulted in the rehabilitation of rivers. Thus, here we aimed to identify major gaps in the biological assessment and rehabilitation of rivers worldwide by focusing on the best examples in Asia, Europe, Oceania, and North, Central, and South America. Our study showed that it is not possible so far to draw a world map of the ecological quality of rivers. Biological assessment of rivers and streams is only implemented officially nation-wide and regularly in the European Union, Japan, Republic of Korea, South Africa, and the USA. In Australia, Canada, China, New Zealand, and Singapore it has been implemented officially at the state/province level (in some cases using common protocols) or in major catchments or even only once at the national level to define reference conditions (Australia). In other cases, biological monitoring is driven by a specific problem, impact assessments, water licenses, or the need to rehabilitate a river or a river section (as in Brazil, South Korea, China, Canada, Japan, Australia). In some countries monitoring programs have only been explored by research teams mostly at the catchment or local level (e.g., Brazil, Mexico, Chile, China, India, Malaysia, Thailand, Vietnam) or implemented by citizen science groups (e.g., Southern Africa, Gambia, East Africa, Australia, Brazil, Canada). The existing large-extent assessments show a striking loss of biodiversity in the last 2-3 decades in Japanese and New Zealand rivers (e.g., 42% and 70% of fish species threatened or endangered, respectively). A poor condition (below Good condition) exists in 25% of South Korean rivers, half of the European water bodies, and 44% of USA rivers, while in Australia 30% of the reaches sampled were significantly impaired in 2006. Regarding river rehabilitation, the greatest implementation has occurred in North America, Australia, Northern Europe, Japan, Singapore, and the Republic of Korea. Most rehabilitation measures have been related to improving water quality and river connectivity for fish or the improvement of riparian vegetation. The limited extent of most rehabilitation measures (i.e., not considering the entire catchment) often constrains the improvement of biological condition. Yet, many rehabilitation projects also lack pre-and/or post-monitoring of ecological condition, which prevents assessing the success and shortcomings of the recovery measures. Economic constraints are the most cited limitation for implementing monitoring programs and rehabilitation actions, followed by technical limitations, limited knowledge of the fauna and flora and their life-history traits (especially in Africa, South America and Mexico), and poor awareness by decision-makers. On the other hand, citizen involvement is recognized as key to the success and sustainability of rehabilitation projects. Thus, establishing rehabilitation needs, defining clear goals, tracking progress towards achieving them, and involving local populations and stakeholders are key recommendations for rehabilitation projects (Table 1). Large-extent and long-term monitoring programs are also essential to provide a realistic overview of the condition of rivers worldwide. Soon, the use of DNA biological samples and eDNA to investigate aquatic diversity could contribute to reducing costs and thus increase monitoring efforts and a more complete assessment of biodiversity. Finally, we propose developing transcontinental teams to elaborate and improve technical guidelines for implementing biological monitoring programs and river rehabilitation and establishing common financial and technical frameworks for managing international catchments. We also recommend providing such expert teams through the United Nations Environment Program to aid the extension of biomonitoring, bioassessment, and river rehabilitation knowledge globally.

Primary and secondary oocyte growth dynamics in anadromous semelparous Allis shad Alosa alosa.

We analysed the ovarian dynamics of the anadromous semelparous allis shad Alosa alosa for which our working hypothesis was that mature pre-spawning females would have very low or even exhausted primary growth (PG) oocyte reserves; semelparity has been linked with the depletion of the pool of PG oocytes. To test this hypothesis, the PG oocytes were enumerated, their recruitment pattern to the secondary growth (SG) phase was analysed and their potential replenishment from the pool of oogonia was examined in females caught very close to the Mondego River mouth, in central Portugal and along the river. The development of the SG oocytes was also analysed, the fecundity (batch, total and annual) values were estimated and the intensity of atresia was quantified. Ovarian samples and histological sections were investigated in parallel. A dynamic recruitment pattern of PG oocytes to the SG phase was revealed, where all PG oocytes were recruited and were not replenished by oogonia. Annual fecundity was subject to down-regulation due to atresia prior to spawning and its size was multiple times higher than the size of batch fecundity. Lack of population synchronicity in ovarian development and spawning migration was also observed. This multifaceted analysis of the ovarian dynamics of this species will contribute to management efforts for this critically endangered and economically important fish throughout its geographical distribution. The results reported in this study will also assist in unravelling the complexity of the early processes of oogenesis in fish.

Muscle fatty acid profiles of sea lamprey (Petromyzon marinus L.) indicate the use of fast metabolized energy during ontogenesis.

A comprehensive characterization of muscle's FA composition of sea lamprey ammocoetes and adults was performed to test the hypothesis that larvae, and early spawning migrants have a similar FA profile prior to metamorphosis and to spawning migration. Subsequently, the role played by FA signature in these two highly demanding stages of life cycle was inferred. The results confirm that muscle represents an important fat reservoir, and the FA trophic markers revealed the importance of bacteria as sources of iso and anteiso FA and the strong trophic representation of benthic phytoplankton (diatoms) to larvae muscle FA profile. In early spawning migrants, the significance of marine food web to FA muscle profile is highlighted by the presence of FA signatures characteristics of herbivorous calanoid copepods. Although both life cycle phases studied do not share the same muscle FA signature, there is a part of the profile that is common, which is characterized by FA used in ß-oxidation, such as C18:1ω9 but also by medium chain FA and PUFA which points that PUFA are spared as fuel to ß-oxidation process and probably used to the development of tissues membranes (ammocoetes) and gonadal development and eicosanoid production among others (early spawning migrants). Further studies on FA profile are necessary to elucidate the FA role either during different life stages (ontogeny) or in the distinct habitats frequented (freshwater versus marine) by this diadromous species.

European Lampreys: New Insights on Postglacial Colonization, Gene Flow and Speciation.

Ice ages are known to be the most dominant palaeoclimatic feature occurring on Earth, producing severe climatic oscillations and consequently shaping the distribution and the population structure of several species. Lampreys constitute excellent models to study the colonization of freshwater systems, as they commonly appear in pairs of closely related species of anadromous versus freshwater resident adults, thus having the ability to colonize new habitats, through the anadromous species, and establish freshwater resident derivates. We used 10 microsatellite loci to investigate the spatial structure, patterns of gene flow and migration routes of Lampetra populations in Europe. We sampled 11 populations including the migratory L. fluviatilis and four resident species, L. planeri, L. alavariensis, L. auremensis and L. lusitanica, the last three endemic to the Iberian Peninsula. In this southern glacial refugium almost all sampled populations represent a distinct genetic cluster, showing high levels of allopatric differentiation, reflecting long periods of isolation. As result of their more recent common ancestor, populations from northern Europe are less divergent among them, they are represented by fewer genetic clusters, and there is evidence of strong recent gene flow among populations. These previously glaciated areas from northern Europe may have been colonized from lampreys expanding out of the Iberian refugia. The pair L. fluviatilis/L. planeri is apparently at different stages of speciation in different locations, showing evidences of high reproductive isolation in the southern refugium, and low differentiation in the north.

Movements of Diplodus sargus (Sparidae) within a Portuguese coastal Marine Protected Area: Are they really protected?

Mark-recapture tagging and acoustic telemetry were used to study the movements of Diplodus sargus within the Pessegueiro Island no-take Marine Protected Area (MPA), (Portugal) and assess its size adequacy for this species' protection against fishing activities. Therefore, 894 Diplodus sargus were captured and marked with conventional plastic t-bar tags. At the same time, 19 D. sargus were tagged with acoustic transmitters and monitored by 20 automatic acoustic receivers inside the no-take MPA for 60 days. Recapture rate of conventionally tagged specimens was 3.47%, most occurring during subsequent marking campaigns. One individual however was recaptured by recreational fishermen near Faro (ca. 250 km from the tagging location) 6 months after release. Furthermore, three specimens were recaptured in October 2013 near releasing site, one year after being tagged. Regarding acoustic telemetry, 18 specimens were detected by the receivers during most of the study period. To analyse no-take MPA use, the study site was divided into five areas reflecting habitat characteristics, three of which were frequently used by the tagged fish: Exterior, Interior Protected and Interior Exposed areas. Information on no-take protected area use was also analysed according to diel and tidal patterns. Preferred passageways and permanence areas were identified and high site fidelity was confirmed. The interaction between tide and time of day influenced space use patterns, with higher and more variable movements during daytime and neap tides. This no-take MPA proved to be an important refuge and feeding area for this species, encompassing most of the home ranges of tagged specimens. Therefore, it is likely that this no-take MPA is of adequate size to protect D. sargus against fishing activities, thus contributing to its sustainable management in the region.

Structural lipid changes and Na(+)/K(+)-ATPase activity of gill cells' basolateral membranes during saltwater acclimation in sea lamprey (Petromyzon marinus, L.) juveniles.

Seawater acclimation is a critical period for anadromous species and a process yet to be understood in lampreys. Considering that changes in lipid composition of the gill cells' basolateral membranes may disrupt the major transporter Na(+)K(+)-ATPase, the goal of this study was to detect changes at this level during juvenile sea lamprey seawater acclimation. The results showed that saltwater acclimation has a direct effect on the fatty acid composition of gill cells basolateral membrane's phospholipids. When held in full-strength seawater, the fatty acid profile of basolateral membrane's phospholipids suffered a restructure by increasing either saturation or the ratio between oleic acid and eicosapentaenoic acid. Simultaneously, the activity of Na(+)K(+)-ATPase revealed a significant and positive correlation with basolateral membrane's cholesterol content in the presence of highest salinity. Our results pointed out for lipid adjustments involving the functional transporter present on the gill cell basolateral membranes to ensure the role played by branchial Na(+)K(+)-ATPase in ion transport during saltwater acclimation process. The responses observed contributed to the strategy adopted by gill cell's basolateral membranes to compensate for osmotic and ionic stressors, to ensure the success of the process of seawater acclimation associated with the downstream trophic migration of juvenile sea lamprey.

Investigating population structure of Sea Lamprey (Petromyzon marinus, L.) in Western Iberian Peninsula using morphological characters and heart fatty acid signature analyses.

This study hypothesizes the existence of three groups of sea lamprey Petromyzon marinus L. in Portugal (North/Central group, Tagus group, and Guadiana group), possibly promoted by seabed topography isolation during the oceanic phase of the life cycle. Within this context, our purpose was to analyze the existence of a stock structure on sea lamprey populations sampled in the major Portuguese river basins using both morphological characters and heart tissue fatty acid signature. In both cases, the multiple discriminant analysis revealed statistically significant differences among groups, and the overall corrected classification rate estimated from cross-validation procedure was particularly high for the cardiac muscle fatty acid profiles (i.e. 83.8%). Morphometric characters were much more useful than meristic ones to discriminate stocks, and the most important variables for group differentiation were eye length, second dorsal fin length and branchial length. Fatty acid analysis showed that all lampreys from the southern Guadiana group were correctly classified and not mixing with individuals from any other group, reflecting a typical heart fatty acid signature. Our results revealed that 89.5% and 72.2% of the individuals from the Tagus and North/Central groups, respectively, were also correctly classified, despite some degree of overlap between individuals from these groups. The fatty acids that contributed to the observed segregation were C16:0; C17:0; C18:1ω9; C20:3ω6 and C22:2ω6. Detected differences are probably related with environmental variables to which lampreys may have been exposed, which leaded to different patterns of gene expression. These results suggest the existence of three different sea lamprey stocks in Portugal, with implication in terms of management and conservation.

Strong genome-wide divergence between sympatric European river and brook lampreys.

Lampreys, together with hagfishes, are the only extant representatives of jawless vertebrates and thus of prime interest for the study of vertebrate evolution [1]. Most lamprey genera occur in two forms with divergent life histories: a parasitic, anadromous and a non-parasitic, freshwater resident form [2-8]. The taxonomic status of such 'paired species' is disputed, however. While indistinguishable at larval stages, but clearly distinct as adults, they cannot be differentiated with available genetic data [6,7], which has fuelled speculations that the two forms may in fact represent products of phenotypic plasticity within a single species. Here, we use restriction site-associated DNA sequencing (RADseq) to examine the genetic population structure of sympatric European river (Lampetra fluviatilis L., 1758) and brook (Lampetra planeri Bloch, 1784) lampreys. We find strong genetic differentiation and identify numerous fixed and diagnostic single nucleotide polymorphisms (SNPs) between the two species, 12 of which can be unequivocally assigned to specific genes.