Molecular phylogeography reveals multiple Pleistocene divergence events in estuarine crabs from the tropical West Pacific

Due to the lack of visible barriers to gene flow, it was a long-standing assumption that marine coastal species are widely distributed, until molecular studies revealed geographically structured intraspecific genetic differentiation in many taxa. Historical events of sea level changes during glacial periods are known to have triggered sequential disjunctions and genetic divergences among populations, especially of coastal organisms. The Parasesarma bidens species complex so far includes three named plus potentially cryptic species of estuarine brachyuran crabs, distributed along East to Southeast Asia. The aim of the present study is to address phylogeography and uncover real and hidden biological diversity within this complex, by revealing the underlying genetic structure of populations and species throughout their distribution ranges from Japan to West Papua, with a comparison of mitochondrial COX1 and 16S rRNA gene sequences. Our results reveal that the P. bidens species complex consists of at least five distinct clades, resulting from four main cladogenesis events during the mid to late Pleistocene. Among those clades, P. cricotum and P. sanguimanus are recovered as monophyletic taxa. Geographically restricted endemic clades are encountered in southeastern Indonesia, Japan and China respectively, whereas the Philippines and Taiwan share two clades. As individuals of the Japanese clade can also be found in Taiwan, we provide evidence of a third lineage and the occurrence of a potential cryptic species on this island. Ocean level retreats during Pleistocene ice ages and present oceanic currents appear to be the main triggers for the divergences of the five clades that are here addressed as the P. bidens complex. Secondary range expansions converted Taiwan into the point of maximal overlap, sharing populations with Japan and the Philippines, but not with mainland China.

SEALNET: Facial recognition software for ecological studies of harbor seals

Methods for long-term monitoring of coastal species such as harbor seals, are often costly, time-consuming, and highly invasive, underscoring the need for improved techniques for data collection and analysis. Here, we propose the use of automated facial recognition technology for identification of individual seals and demonstrate its utility in ecological and population studies. We created a software package, SealNet, that automates photo identification of seals, using a graphical user interface (GUI) software to identify, align and chip seal faces from photographs and a deep convolutional neural network (CNN) suitable for small datasets (e.g., 100 seals with five photos per seal). We piloted the SealNet technology with a population of harbor seals located within Casco Bay on the coast of Maine, USA. Across two-years of sampling, 2019 and 2020, at seven haul-out sites in Middle Bay, we processed 1529 images representing 408 individual seals and achieved 88% (93%) rank-1 accuracy in closed set (open set) seal identification. We identified four seals that were photographed in both years at neighboring haul-out sites, suggesting that some harbor seals exhibit site fidelity within local bays across years, and that there may be evidence of spatial connectivity among haul-out sites. Using capture-mark-recapture (CMR) calculations, we obtained a rough preliminary population estimate of 4386 seals in the Middle Bay area. SealNet software outperformed a similar face recognition method developed for primates, PrimNet, in identifying seals following training on our seal dataset. The ease and wealth of image data that can be processed using SealNet software contributes a vital tool for ecological and behavioral studies of marine mammals in the emerging field of conservation technology.

Do Hydrothermal Shrimp Smell Vents?

Deep-sea species endemic to hydrothermal vents face the critical challenge of detecting active sites in a vast environment devoid of sunlight. This certainly requires specific sensory abilities, among which olfaction could be a relevant sensory modality, since chemical compounds in hydrothermal fluids or food odors could potentially serve as orientation cues. The temperature of the vent fluid might also be used for locating vent sites. The objective of this study is to observe the following key behaviors of olfaction in hydrothermal shrimp, which could provide an insight into their olfactory capacities: (1) grooming behavior; (2) attraction to environmental cues (food odors and fluid markers). We designed experiments at both deep-sea and atmospheric pressure to assess the behavior of the vent shrimp Rimicaris exoculata and Mirocaris fortunata, as well as of the coastal species Palaemon elegans and Palaemon serratus for comparison. Here, we show that hydrothermal shrimp groom their sensory appendages similarly to other crustaceans, but this does not clean the dense bacterial biofilm that covers the olfactory structures. These shrimp have previously been shown to possess functional sensory structures, and to detect the environmental olfactory signals tested, but we do not observe significant attraction behavior here. Only temperature, as a signature of vent fluids, clearly attracts vent shrimp and thus is confirmed to be a relevant signal for orientation in their environment.

Mapping global inputs and impacts from of human sewage in coastal ecosystems

Coastal marine ecosystems face a host of pressures from both offshore and land-based human activity. Research on terrestrial threats to coastal ecosystems has primarily focused on agricultural runoff, specifically showcasing how fertilizers and livestock waste create coastal eutrophication, harmful algae blooms, or hypoxic or anoxic zones. These impacts not only harm coastal species and ecosystems but also impact human health and economic activities. Few studies have assessed impacts of human wastewater on coastal ecosystems and community health. As such, we lack a comprehensive, fine-resolution, global assessment of human sewage inputs that captures both pathogens and nutrient flows to coastal waters and the potential impacts on coastal ecosystems. To address this gap, we use a new high-resolution geospatial model to measure and map nitrogen (N) and pathogen—fecal indicator organisms (FIO)—inputs from human sewage for ~135,000 watersheds globally. Because solutions depend on the source, we separate nitrogen and pathogen inputs from sewer, septic, and direct inputs. Our model indicates that wastewater adds 6.2Tg nitrogen into coastal waters, which is approximately 40% of total nitrogen from agriculture. Of total wastewater N, 63% (3.9Tg N) comes from sewered systems, 5% (0.3Tg N) from septic, and 32% (2.0Tg N) from direct input. We find that just 25 watersheds contribute nearly half of all wastewater N, but wastewater impacts most coastlines globally, with sewered, septic, and untreated wastewater inputs varying greatly across watersheds and by country. Importantly, model results find that 58% of coral and 88% of seagrass beds are exposed to wastewater N input. Across watersheds, N and FIO inputs are generally correlated. However, our model identifies important fine-grained spatial heterogeneity that highlight potential tradeoffs and synergies essential for management actions. Reducing impacts of nitrogen and pathogens on coastal ecosystems requires a greater focus on where wastewater inputs vary across the planet. Researchers and practitioners can also overlay these global, high resolution, wastewater input maps with maps describing the distribution of habitats and species, including humans, to determine the where the impacts of wastewater pressures are highest. This will help prioritize conservation efforts.Without such information, coastal ecosystems and the human communities that depend on them will remain imperiled.

Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant

Several past and recent climatic and geological events have greatly influenced the current distribution of coastal species around the Mediterranean Basin. As a consequence, the reconstruction of the distributional history of these species is challenging. In this study, we used both chloroplast and nuclear SNPs to assess the levels of genetic differentiation, contemporary/historical levels of gene flow, and demographic history for the three only known (one mainland and two insular) populations of Eokochia saxicola, a rare Mediterranean coastal rocky halophyte. Plastid genome analysis revealed very low intraspecific haplotype variation and partial admixture among Capri and Palinuro populations with at least two independent colonization events for the Strombolicchio islet. Nuclear SNPs variation consistently identified three distinct genetic clusters corresponding to our sampling localities. Furthermore, strong genetic isolation was confirmed by both historical and contemporary levels of migration among the three populations. The DIYABC analysis identified two introductions temporally separated from Palinuro to Capri (ca.25 Mya) and subsequently to Strombolicchio (ca.09 Mya) as the most likely hypothesis for the current distribution of E. saxicola. Regardless of their small population sizes, all study sites supported high-genetic diversity maintained by outcrossing and random mating between individuals owing largely to wind pollination, an exclusive trait among Mediterranean narrow endemics. In conclusion, the patterns observed confirm that some Mediterranean endemics are not necessarily “evolutionary dead-ends” but rather represent species that have extensive demographic stability and a strong evolutionary legacy.

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to temperate iron-poor oceans revealed by a chromosome-scale genome sequence.

Eukaryotic phytoplankton are key actors in marine ecosystems, they contribute to atmospheric CO2 sequestration and supply organic matter to the trophic network. Among them, Pelagophytes (Stramenopiles) algae are a diverse class with coastal species causative of harmful algal blooms while others are cosmopolites and abundant in open ocean ecosystems. Despite their ecological importance, only a few genomic references exist limiting our capacity to identify them and study their adaptation mechanisms in a changing environment. Here, we report the complete chromosome-scale assembled genome sequence of Pelagomonas calceolata. We identified unusual large low-GC and gene-rich regions potentially hosting centromeres. These particular genomic structures could be explained by the absence of genes necessary for an important recombination pathway in this species. We identified a large repertoire of genes involved in inorganic nitrogen sensing and uptake as well as many genes replacing iron-required proteins potentially explaining its ecological success in oligotrophic waters. Finally, based on this high-quality assembly, we evaluated P. calceolata relative abundance in all oceans using environmental Tara datasets. Our results suggest that P. calceolata is one of the most abundant eukaryote species in the oceans with a relative abundance driven by the high temperature and iron-poor conditions. Collectively, these findings bring new insights into the biology and ecology of P. calceolata and lay the foundation for the analysis of the adaptation and acclimation strategy of this picophytoplankton.

Litter Mixing Effect On Decomposition Rate And Nutrient Release: Low-Quality Leaves of Coastal Species

Coastal wetlands are among the most carbon-rich ecosystems in the world. Litter decomposition is a major process controlling soil carbon input. Litter mixing has shown a non-additive effect on the litter decomposition of terrestrial plants particularly of those species having contrasting litter quality. But the non-additive effect has been rarely tested in coastal plants. We selected three common mangrove species and one saltmarsh species, co-occurring in subtropical coasts, to test whether the non-additive effect occurs when the litters of these coastal species mixing together. We are also concerned whether the changes in the decomposition rate of litter will affect the nutrient contents in waters. A litter-bag experiment was carried out in a glasshouse with single and mixed leaf litters. A non-additive effect was observed in the litter mixtures of mangrove species Aegiceras corniculatum vs. Kandelia obovata (antagonistic) and A. corniculatum vs. Avicennia marina (synergistic). Whereas, the mixture of A. corniculatum (mangrove species) and Spartina alterniflora (saltmarsh species) showed an additive effect. The strength of the non-additive effect was unrelated to the initial trait dissimilarity of litters. Instead, the decomposition rate and mass remaining of litter mixtures were strongly related to the carbon concentrations in litters. Nutrient content in waters was dependent on the decomposition rate of litter mixtures but not on the initial nutrient concentrations in litters. Despite the behind mechanisms were not yet revealed by the current study, these findings have improved our understanding of the litter decomposition of coastal species and the consequent nutrient release.

Mercury levels in Tarmat Contaminated Beaches and its Marine Organisms living along the Qatari Coasts

One of the pollutants that affects the coastal environment of Qatar is the vast expanse of oil residue ‘tarmats’ deposited on its beaches. The current study is aimed at gauging the concentration levels of total mercury (THg) in tarmat contaminated sediments and test their presence in selected coastal species. Three biota classes (Gastropoda, Bivalvia, and Crustacea) have been found on the tarmat of Ras Rakan and Umm Tais islands. Layers of hard asphalt-like tarmats and sediments samples were collected from 34 sites, along the coast of Qatar. Moreover, the Biota Sediment Accumulation Factor (BSAF) was calculated for THg through sentinel species. The mean concentrations of THg is 0.089 ± 0.02 μg.g-1. Compared to earlier studies, a relatively higher concentration of THg (0.463 μg.g-1) had been observed.