Genetic diversity and connectivity remain high in Holothuria polii (Delle Chiaje 1823) across a coastal lagoon-open sea environmental gradient

A peek into the population genetics of white teatfish (Holothuria fuscogilva) of Kenya's south coast

BACKGROUND

The white teatfish, Holothuria fuscogilva, is widely distributed in coastal areas, including waters around coral reefs and seagrasses in the Indo-Pacific. In Kenya, the species is distributed in shallow reefs with higher landings reported from the Vanga-Shimoni-Gazi seascape on the Kenyan south coast. Despite its high exploitation for export and its vulnerable and endangered statuses under IUCN and CITES respectively, Kenya's H. fuscogilva populations and how they may have been impacted by the fishing pressure have not been studied.

METHODS

We estimated the genetic diversity and structure of H. fuscogilva population conveniently sampled from three sites in Kenyan south coast using the mitochondrial cytochrome oxidase subunit I (COI) gene sequences. We recorded 30 haplotypes with 43 polymorphic sites across the population. Furthermore, we estimated an overall high haplotype diversity and low nucleotide diversity of estimates of h = 0.970 ± 0.013 and π = 0.010 ± 0.001 respectively.

CONCLUSIONS

These preliminary findings suggest several population outcomes, among them a fit population, which require confirming with more comprehensive study to inform strategies for the sustainable exploitation and management of the species.

Unstable environment of coastal lagoons drives genetic variation in the amphipod Quadrivisio lutzi

The freshwater/brackish amphipod Quadrivisio lutzi inhabits coastal lagoons, highly unstable environments subject to sudden inflow of marine water. Our aim was to evaluate how the genetic composition varies in these populations. Brazilian populations were compared by 16S rRNA and COI gene sequences. The genetic structure of four Rio de Janeiro amphipod populations was evaluated during the period of 2011-2019 by COI. Rio de Janeiro population was compared with Alagoas and São Paulo populations, which was genetically distinct, at species level (16S, d > 7%; COI, d >14%). The genetic structure in Rio de Janeiro showed the Imboassica subpopulation as the most divergent (Imboassica & Carapebus, F ST = 0.238), followed by Lagamar population (Lagamar & Carapebus, F ST = 0.049). The geographic distance and urbanization around these lagoons explain the degree of genetic isolation of these amphipod subpopulations. Paulista and Carapebus populations were not structured. Temporal variation in haplotype number and frequency were evident in both populations that were evaluated (Carapebus and Imboassica). Changes in salinity and water volume variation at these lagoons may be responsible for the observed changes in genetic composition, which may be the results of genetic drift effects over temporally fluctuating size subpopulations, without loss of genetic diversity.

Recolonization origin and reproductive locations, but not isolation from the sea, lead to genetic structure in migratory lagoonal fishes

The assessment of connectivity in marine ecosystems is a requirement to adequate fisheries management. In this study we have selected two commercially exploited migratory species, European perch (Perca fluviatilis) and European smelt (Osmerus eperlanus), to evaluate the connectivity between the Curonian Lagoon and the coastal Baltic Sea. Our results indicate that isolation between the coastal lagoon and the adjacent sea area does not lead to the formation of genetic structure in migratory fish species. However, both species do register subpopulations coexisting in the area without interbreeding. This indicates that the fisheries management for migratory fishes in coastal lagoons affects a wider area than just the coastal lagoon. European perch, being a postglacial recolonizer from various refugees, has four different subpopulations, while the mechanism that maintains this division remains unexplored. The feeding migrations of European perch to the coastal zone suggest that the reproduction might occur elsewhere and that the factors for genetic structure suggested at the Baltic Sea scale might operate during these migrations. For European smelt, we discuss the existence of two different ecotypes, one lagoonal and one diadromous, and the different registered spawning locations as explicative causes for the maintenance of two genetically divergent clusters. The lagoonal ecotype reproduces and spawns inside the Curonian Lagoon while the diadromous one lives in the open Baltic Sea, performing spawning migrations to the lagoon and the mouth of Nemunas river, thus, maintaining the genetic divergence among them. However, our results indicate that there are no differences in size between both clusters, while the lagoonal population is expected to be smaller, forbidding the determination of two genetically different ecotypes. We conclude that there are no geographically and genetically separated populations of these two species in the lagoon-sea- terrestrial inlets continuum, and unified stock management for the coastal Baltic Sea and the Curonian lagoon is required.

Comparing genetic markers’ efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori

Sea cucumber (bêche-de-mer, Echinodermata: Holothuroidea) is one of the top internationally traded seafood varieties. Besides its direct nutritional benefits, it is continuously used in the traditional medicine in different areas and cultures in the world. This world-wide interest triggered various issues related to stocks´ declining and risks of species extinction. For these reasons, the current study was designed to provide molecular tools for accurate discrimination between two sea cucumber species that prevail the Mediterranean of these echinoderms in Egypt, that are Holothuria polii and H. sanctori. The power of three gene markers, i.e., 16S rDNA, 28S rDNA, and Histone H3 in achieving accurate DNA-based identification, as well as elucidating clear phylogenetic and genetic diversity differences between those two species was assessed. Among the three genes, 16S rDNA showed the highest potentials as genetic and phylogenetic species discrimination marker. Both 28S rDNA and H3 exhibited the least number of holothuroid reference sequences in the GenBank database. For genetic diversity within each species population, 16S rDNA exhibited the best potentials, followed by H3. 28S rDNA showed no genetic polymorphism at all. Moreover, the collective data of both H3 and 16S rDNA suggested a possible role of asexual reproduction behavior in H. sanctori in the reduction of genetic diversity, as a possible response to overfishing. Hence, the current research can recommend the simultaneous application of both 16S rDNA and H3 as accurate markers for genetic discrimination among H. polii, H. sanctori and other different holothuroid species.  

Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae)

The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.

Genetic structure of the long-snouted seahorse, Hippocampus guttulatus, in the Central–Western Mediterranean Sea

The seahorse Hippocampus guttulatus reaches its highest abundance in confined environments, where it has unique biological and ecological traits that suggest significant genetic differentiation among populations. In the present study, we aimed to reveal the genetic structure of this species by analysing eight microsatellite loci and a mitochondrial DNA region (cytochrome b) of eight populations from the Central–Western Mediterranean Sea, including lagoon sites. Levels of genetic diversity, as measured by the total number of alleles, number of private alleles, allelic richness and heterozygosity, ranged from low to moderate. The overall value of inbreeding was high, indicating a deficiency in heterozygotes. The haplotype network had a star-like construction, with the most common haplotype present in all populations. Data from the two molecular markers congruently displayed a similar pattern and revealed low genetic differentiation, notwithstanding predictions based on species traits. The observed genetic structure is probably the result of both historical population demographic events and current gene flow. The investigated lagoons, however, revealed a unique genetic profile, which is especially highlighted by the Taranto population. At this site, the results also showed altered values of observed/expected heterozygosity and allelic richness, a characteristic of marginal populations. Our study suggests that lagoon populations should be managed as distinct genetic units.

Microscopic ossicle analyses and the complete mitochondrial genome sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea) provide new information to support the phylogenetic positioning of this sea cucumber species

Sea cucumbers (Holothuroidea) are ecologically important organisms for their bioturbation and alkalinization activities of the seabed. These species are extensively fished as they are considered luxury food. Sea cucumbers are also relevant for biomedical studies and the production of bioactive compounds. A few initiatives are recently evaluating sea cucumbers as novel aquaculture species. The aim of this study was to provide morphological and genetic information useful for the identification of Holothuria polii, the white spot sea cucumber (a common species of the Mediterranean Sea). We generated the complete sequence of the mitochondrial DNA (mtDNA) genome of this species and combined it with a detailed ossicle characterization of the sequenced specimen by scanning electron microscopic analysis. Ossicles (known also as sclerites) are anatomical features that can discriminate Holothuroidea species, including the closely related ones of the genus Holothuria. The complete mitochondrial genome was assembled, functionally annotated and then used to evaluate the phylogenetic relationship of H. polii against the other few Holothuroidea species for which the whole mtDNA was available. The 15,907 bp H. polii mtDNA sequence has the same gene order already reported for H. scabra, H. forskali and other species of the same class. Cox1 and 16S gene sequences were informative for species identification across the genus and could be used for the authentication of commercialized Holothuria spp. The mitochondrial genome sequence presented here provides the basis to a future analysis of the variability of H. polii populations in the Mediterranean region.

Anti-proliferative and anti-inflammatory activities of the sea cucumber Holothuria polii aqueous extract

Objective:

Sea cucumbers are considered among the most important functional foods. Following bioassay guided fractionation, we assessed the anti-proliferative and anti-inflammatory activities of Holothuria polii (H. polii) extracts.

Methods:

Sea cucumber ethanolic extract and the partially purified aqueous fractions were assessed for their anti-proliferative activities. These latter bioactivities were evaluated in the highly invasive MDA-MB-231 human breast cancer cells in two-dimensional and three-dimensional cultures using trypan blue exclusion assay. The tumor-suppressive effects of sea cucumber ethanolic extract and aqueous fractions were assayed by measuring the trans-well invasion of MDA-MB-231 cells and the expression of some epithelial mesenchymal transition markers using quantitative reverse-transcription polymerase chain reaction and western blot analysis. The anti-inflammatory activity of the aqueous fraction was tested by measuring the secreted levels of interleukin-6, nitric oxide, and matrix metalloproteinase 9 in endotoxin-induced mammary epithelial SCp2 cells and interleukin-1β in phorbol-12-myristate-13-acetate-activated human monocytic THP-1 cells.

Results:

Sea cucumber ethanolic extract and the aqueous fraction significantly decreased the proliferation of MDA-MB-231 cells by more than 50% at similar and noncytotoxic concentrations and caused an arrest in the S-phase of the cell cycle of treated cells. In contrast, petroleum ether, chloroform, ethyl acetate, and n-butanol organic fractions did not show any significant activity. Furthermore, sea cucumber ethanolic extract and aqueous fraction reduced the proliferation of MDA-MB-231 cells in three-dimensional cultures by more than 60% at noncytotoxic concentrations. In addition, treatment with these concentrations resulted in the loss of stellate outgrowths in favor of spherical aggregates and a 30% decrease in invasive properties. Both sea cucumber ethanolic extract and aqueous decreased the transcription of vimentin and the protein expression levels of vimentin and N-cadherin in three-dimensional cultures. The aqueous fraction decreased the levels of inflammatory markers interleukin-6, nitric oxide, and matrix metalloproteinase 9 in the mouse mammary SCp2 cells, and the level of interleukin-1β produced by phorbol-12-myristate-13-acetate-activated THP-1 human monocytic cells.

Conclusion:

The data reveal for the first time promising anti-proliferative and anti-inflammatory activities in H. polii water extract in two-dimensional and three-dimensional culture models.

Genetic structure of Japanese sea cucumbers (Apostichopus japonicus) along the Sanriku coast supports the effect of earthquakes and related tsunamis

The Japanese common sea cucumber (Apostichopus japonicus) is a major marine product from Sanriku, Japan, but its populations were severely affected by the 2011 Tohoku earthquake, possibly decreasing its genetic diversity and increasing its extinction risk. In this study, we estimated the genetic structure and diversity of sea cucumbers from Touni and Yamada Bays of Sanriku over 4 years after the earthquake. The between-population genetic structure was estimated using two mitochondrial DNA regions (cytochrome c oxidase subunit I and 16S rDNA). Genetic differentiation (as measured by pairwise F_ST) was not significant between locations. Thus, even after the tsunami, gene flow and genetic diversity among the two sea cucumber populations were maintained. Our data also suggested that sea cucumbers in Sanriku experienced population expansion of about 0.20-0.24 million years ago, during the stable Mindel-Riss interglacial period. We conclude that A. japonicus populations in Sanriku could maintain their genetic structure throughout multiple disastrous tsunamis over the past several 1000 years. The high dispersal ability of planktonic larvae may enable the entrance of new recruits, thereby reducing risks associated with genetic structure and diversity changes stemming from mass die-offs in a given body of water from the past to the present.

Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan

The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.

Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda)

We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (π_syn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m². Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10⁻⁵ per site per year or μ = 1.99 × 10⁻⁴ mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (N_e = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.

Structure elucidation, protein profile and the antitumor effect of the biological active substance extracted from sea cucumber Holothuria polii

Holothuria polii (Delle Chiaje, 1823) (Holothuriidae) is a sea cucumber inhabiting Mediterranean Sea coast of Egypt. The bioactive compound of its tegument has antifungal, antibacterial and antiparasitic effects. The present study aims to elucidate the structure of the bioactive material of H. polii for pharmacological and chemotaxonomic purposes. Furthermore, the study demonstrates its efficacy as a cytotoxic agents against two tumor cell lines HCT116 (colon adenocarcinoma cell line) and MCF7 (breast adenocarcinoma cell line). The biological active compound of the ethanol extract has been characterized by means of infrared (IR), proton-nuclear magnetic resonance ((1)H NMR), ultraviolet-visible (UV-Vis) and mass spectra. Protein profile was carried out using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Cytotoxic activity was carried out according to sulforhodamine-B assay. IR, (1)H NMR, UV-Vis and mass spectra showed that the extracted bioactive material is a nonsulfated hexaosides called bivittoside. This glycoside is composed of aglycone and a glycosidic chain (carbohydrate chain) enclosed with six sugar units, including xylose, glucose, 3-O-methylglucose and quinovose. There were no traces of dissolved proteins. The preliminary cytotoxic assay of bivittoside exhibited significant cytotoxic activity against two types of cultured tumor cell lines of HCT116 and MCF7. The half-maximal inhibitory concentration was 17.4 µg/ml and 18 µg/ml for MCF7 and HCT116, respectively. Although H. polii belongs to the genus Holothuria, the lacking of sulfate group and the fact that it contains up to six monosaccharides make it different from this genus. The present study suggests separation of H. polii from its genus to a new one. On the other hand, results support the hypothesis that H. polii bioactive compound has an antitumor effect.