Investigation of mechanisms underlying chaotic genetic patchiness in the intertidal marbled crab Pachygrapsus marmoratus (Brachyura: Grapsidae) across the Ligurian Sea

A multidisciplinary integrated approach using Pachygrapsus marmoratus to assess the impact of port activities on mediterranean marine protected areas

The establishment of marine protected areas is considered the main global strategy to halt the loss of marine biodiversity. Since most of marine areas are open systems, this form of habitat protection cannot prevent their contamination due to human activities performed outside of their borders. Innovative approaches to assess the health status of protected marine habitats are therefore needed. Here we developed a multidisciplinary approach that combines ecological characteristics, bioaccumulation of inorganic and organic pollutants, cell damage (micronuclei frequency, nuclear alterations and LPO) and enzymatic (AChE, CAT, IDH, LDH, GST and CAT) markers focused on an intertidal brachyuran crab, Pachygrapsus marmoratus, to assess the impacts of contaminant exposure on Mediterranean coastal habitats. As study sites we selected two protected areas and two sites within industrial ports of the Ligurian Sea. Our results showed that the selected crab species is an excellent bioindicator. Individuals collected in sites with the highest levels of heavy metal pollution showed the highest signals of stress responses at both cellular and enzymatic levels, coupled with a high incidence of the parasite Sacculina carcini, a signal of impairment of their standard development and reproduction cycle. We could also prove that one of the selected marine protected areas showed the same intensity of impact as its adjacent port site. Our multidisciplinary approach proved to be a valuable tool to assess the environmental quality and health of protected and disturbed Mediterranean coastal environments and to inform efficient management and protection schemes for such habitats.

Differential gene expression and chemical patterns of an intertidal crab inhabiting a polluted port and an adjacent marine protected area

The acquisition of data to safeguard marine protected areas located close to ports is important in order to develop plans that allow effective protection from pollution as well as sustainable development of the port. The area Secche della Meloria is a Marine Protected Area (MPA-MEL) three miles from Livorno Harbour (LH), which is characterized by a long history of pollution. Here we studied the bioaccumulation and transcriptomic patterns of the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) (Crustacea; Brachyura, Grapsidae), inhabiting the two selected sites. Results showed that the two crab populations are significantly different in their chemical composition of trace elements and Polyciclic Aromatic Hydrocarbons (PAHs), and gene expression patterns (1280 DEGs). Enrichment analysis indicated that crabs at LH had the highest stress response genes, and they were associated with higher levels of bioaccumulation detected in body tissues. We are confident that the significant differential gene expression profiles observed between crabs, characterized by significant chemical differences, is associated with responses to contaminant exposure.

Mitonuclear genetic patterns of divergence in the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) along the Turkish seas

Biogeographical transition zones present good opportunities for studying the effect of the past ice ages on genetic structure of species because secondary contact zones of post-glacial lineages can be formed. In this study, we investigated the population genetic structure of the marbled rock crab, Pachygrapsus marmoratus along the coasts of Turkey. We genotyped 334 individuals from the Black Sea, the Turkish Straits System (TSS), the Aegean, and the Eastern Mediterranean basins. In order to reveal its evolutionary history and its population connectivity, we used mitochondrial CO1 region and five microsatellite loci. CO1 analyzes also included 610 additional samples from Genbank, which covered most of its distribution range. Both microsatellites and mtDNA showed decreased diversity in sampling sites of the TSS and the Black Sea as compared to those along the Aegean and the Levantine coasts. There is an especially strong geographical pattern in distributions of haplotypes in mtDNA, most probably as a result of genetic drift in the Black Sea and the Sea of Marmara (SoM). Microsatellite data analyses revealed two genetically distinct clusters of P. marmoratus (clusters C and M). While individuals belonging to cluster C are present in all the sampling locations, those belonging to cluster M are only detected along the Mediterranean coasts including the Aegean and the Levantine basins. These clusters shared similar haplotypes in the Mediterranean. Haplotypes of two sympatric clusters could be similar due to incomplete lineage sorting of ancestral polymorphisms. In order to retrieve the complex demographic history and to investigate evolutionary processes resulting in sympatric clusters in the Aegean Sea and the Levantine basin, mitochondrial markers with faster mutation rates than CO1 and/or SNP data will be useful.

Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner

A long-standing paradox of marine populations is chaotic genetic patchiness (CGP), temporally unstable patterns of genetic differentiation that occur below the geographic scale of effective dispersal. Several mechanisms are hypothesized to explain CGP including natural selection, spatiotemporal fluctuations in larval source populations, self-recruitment, and sweepstake reproduction. Discriminating among them is extremely difficult but is fundamental to understanding how marine organisms reproduce and disperse. Here, we report a notable example of CGP in the Antarctic limpet, an unusually tractable system where multiple confounding explanations can be discounted. Using population genomics, temporally replicated sampling, surface drifters, and forward genetic simulations, we show that CGP likely arises from an extreme sweepstake event together with collective larval dispersal, while selection appears to be unimportant. Our results illustrate the importance of neutral demographic forces in natural populations and have important implications for understanding the recruitment dynamics, population connectivity, local adaptation, and resilience of marine populations.

Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.