Natural or naturalized? Phylogeography suggests that the abundant sea urchin Arbacia lixula is a recent colonizer of the Mediterranean

Population genomic structure of the sea urchin Diadema africanum, a relevant species in the rocky reef systems across the Macaronesian archipelagos

The sea urchin Diadema africanum is a macro-herbivore found in the rocky reef systems of the West African region and Macaronesian archipelagos. Over several decades, high densities of this species have generated marine barrens in certain areas at the Canary Islands. In contrast, more recently, during the last few years, the species has suffered mass mortality events that continue to the present day. In this study, we used 9,109 Single Nucleotide Polymorphisms (SNPs) and a fragment of a mitochondrial gene to evaluate the species' population structure, effects of mass mortalities on its diversity, and potential local adaptation across the Canary Islands and Cabo Verde. Our research provides compelling evidence of low genomic diversity and homogeneity across the studied area for neutral markers, along with recent demographic fluctuations. The high connectivity among distant areas likely allows a rapid recovering of the populations from local mortality events. Interestingly, we also observed genomic sub-structure from 405 SNPs identified as candidate loci under selection for seawater temperature. The lack of divergence among distant sites and the low diversity found can be attributed to the species' divergence from a small ancestral genomic pool, followed by a contemporary demographic expansion, and ongoinggene flow.

Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758)

The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.

Evaluating restriction enzyme selection for reduced representation sequencing in conservation genomics

Conservation genomic studies in non-model organisms generally rely on reduced representation sequencing techniques based on restriction enzymes to identify population structure as well as candidate loci for local adaptation. While the expectation is that the reduced representation of the genome is randomly distributed, the proportion of the genome sampled might depend on the GC content of the recognition site of the restriction enzyme used. Here, we evaluated the distribution and functional composition of loci obtained after a reduced representation approach using Genotyping-by-Sequencing (GBS). To do so, we compared experimental data from two endemic fish species (Symphodus ocellatus and Symphodus tinca, EcoT22I enzyme) and two ecosystem engineer sea urchins (Paracentrotus lividus and Arbacia lixula, ApeKI enzyme). In brief, we mapped the sequenced loci to the phylogenetically closest reference genome available (Labrus bergylta in the fish and Strongylocentrotus purpuratus in the sea urchin datasets), classified them as exonic, intronic and intergenic, and studied their function by using Gene Ontology (GO) terms. We also simulated the effect of using both enzymes in the two reference genomes. In both simulated and experimental data, we detected an enrichment towards exonic or intergenic regions depending on the restriction enzyme used and failed to detect differences between total loci and candidate loci for adaptation in the empirical dataset. Most of the functions assigned to the mapped loci were shared between the four species and involved a myriad of general functions. Our results highlight the importance of restriction enzyme selection and the need for high-quality annotated genomes in conservation genomic studies.

Brazilian marine phylogeography: A literature synthesis and analysis of barriers

In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.

Acclimation to low pH does not affect the thermal tolerance of Arbacia lixula progeny

As the ocean warms, the thermal tolerance of marine invertebrates is key to determining their distributional change, where acclimation to low pH may impact the thermal range of optimal development. We compared thermal tolerance of progeny from a low pH-acclimated sea urchin (Arbacia lixula) population from the CO₂ vents of Ischia (Italy) and a nearby population living at ambient pH. The percentages of normally developing gastrulae and two-armed larvae were determined across 10 temperatures representing present and future temperature conditions (16-34°C). Vent-acclimated sea urchins showed a greater percentage of normal development at 24 h, with a larger optimal developmental temperature range than control sea urchins (12.3°C versus 5.4°C range, respectively). At 48 h, upper lethal temperatures for 50% survival with respect to ambient temperatures were similar between control (+6.8°C) and vent (+6.2°C) populations. Thus, acclimation to low pH did not impact the broad thermal tolerance of A. lixula progeny. With A. lixula's barrens-forming abilities, its wide thermotolerance and its capacity to acclimate to low pH, this species will continue to be an important ecological engineer in Mediterranean macroalgal ecosystems in a changing ocean.

Predominant east to west colonizations across major oceanic barriers: Insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker

We provide preliminary insights into the global phylogeographic and evolutionary patterns across species of the hydrozoan superfamily Plumularioidea (Cnidaria: Hydrozoa). We analyzed 1,114 16S sequences of 198 putative species of Plumularioidea collected worldwide. We investigated genetic connections and divergence in relation to present-day and ancient biogeographic barriers, climate changes and oceanic circulation. Geographical distributions of most species are generally more constrained than previously assumed. Some species able to raft are dispersed widely. Human-mediated dispersal explains some wide geographical ranges. Trans-Atlantic genetic connections are presently unlikely for most of the tropical-temperate species, but were probably more frequent until the Miocene-Pliocene transition, before restriction of the Tethys Sea and the Central American Seaway. Trans-Atlantic colonizations were predominantly directed westwards through (sub)tropical waters. The Azores were colonized multiple times and through different routes, mainly from the east Atlantic, at least since the Pliocene. Extant geminate clades separated by the Isthmus of Panama have predominantly Atlantic origin. Various ancient colonizations mainly directed from the Indian Ocean to the Atlantic occurred through the Tethys Sea and around South Africa in periods of lower intensity of the Benguela upwelling. Thermal tolerance, population sizes, dispersal strategies, oceanic currents, substrate preference, and land barriers are important factors for dispersal and speciation of marine hydroids.

The Echinoderm Fauna of the Azores (NE Atlantic Ocean)

In more than 150 years of research in the waters surrounding the Azores, several publications on the fauna of echinoderms of the archipelago have been produced, in the form of papers, notes, reports, reviews, and monographs. This work attempts to summarize the present knowledge on this marine group in the Azorean exclusive economic zone (i.e., waters within 200 nautical miles of the archipelago's shores). A short review of the history of the species' taxonomy is given, with key references, geographical distribution, ecology, additional notes and, when possible, figures. We herein report 172 species of echinoderms (6 crinoids, 55 ophiuroids, 45 asteroids, 36 holothurians, and 30 echinoids) from the Azores Archipelago, most of them inhabiting deep waters (>200 m). Only 29 shallow-water species were recorded locally (≤50 m depth). In general, the echinoderm species present in the Azores are characterized by a wide geographical distribution in the Atlantic Ocean. Only nine taxa (all deep-water species, >840 m) appear to be restricted to the Azorean waters. Overall, the knowledge of the echinoderm fauna of the Azores is out-dated, with many species last collected in the archipelago over 100 years ago. A recent interest in the Azorean Mid-Atlantic waters has brought oceanographic cruises back to the archipelago, thus providing new opportunities for the renewal of 150 years of echinoderm studies in the area.

Phylogeographic and evolutionary history analyses of the warty crab Eriphia verrucosa (Decapoda, Brachyura, Eriphiidae) unveil genetic imprints of a late Pleistocene vicariant event across the Gibraltar Strait, erased by postglacial expansion and admixture among refugial lineages

Background

The Pleistocene cyclic sea-level fluctuations are thought to have markedly affected the distribution and genetic architecture of Atlanto-Mediterranean biota. Despite the acknowledged key role played by these historical events in shaping population genetic structure of marine species, little is still known about the processes involved in shaping the spatial distribution of genetic variation within intertidal species. We intended in this study to reconstruct the phylogeography of a common and widely distributed coastal species across the East Atlantic and Mediterranean Sea (the warty crab Eriphia verrucosa), aiming to unravel potential microevolutionary processes likely involved in shaping its genetic polymorphism. For this purpose, a total of 155 specimens of E. verrucosa from 35 locations across the entire distribution range were analyzed by comparing a 453 basepairs region of the mitochondrial gene cytochrome oxidase subunit 1 (Cox1).

Results

Our results unveiled the prevalence of high genetic connectivity among East Atlantic and Mediterranean populations, with noticeable genetic distinctiveness of the peripheral population from the Azores. Spatio-temporal patterns of genetic diversification and demographic history allowed retrieving genetic imprints of late Pleistocene vicariant event across the Gibraltar Strait followed by subsequent postglacial expansion events for both the East Atlantic and Mediterranean regions. Integrative evidences from the outcomes of comparison of regional genetic diversification, as well as evolutionary and biogeographic histories reconstructions, support the existence of potential glacial refugia for E. verrucosa in the East Atlantic and western Mediterranean. Our results also revealed low levels of genetic variability along with recent demographic and spatial expansion events for eastern Mediterranean warty crabs, suggesting that the eastern areas within the distribution range of the species might have been recently colonized from putative glacial refugia.

Conclusions

These findings provide new insights into the phylogeography and evolutionary history of a common but poorly studied Atlanto-Mediterranean decapod species. Specifically, they contribute to the understanding of the impact of historical processes on shaping contemporary population genetic structure and diversity in intertidal marine species.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1423-2) contains supplementary material, which is available to authorized users.

No-take marine reserves control the recovery of sea urchin populations after mass mortality events

Understanding how no-take zones (NTZs) shape the population dynamics of key herbivores is crucial for the conservation and management of temperate benthic communities. Here, we examine the recovery patterns of sea urchin populations following a high-intensity storm under contrasting protection regimes in the NW Mediterranean Sea. We found significant differences in the recovery trends of Paracentrotus lividus abundance and biomass in the five years following the storm. The P. lividus populations outside the NTZ recovered faster than the populations inside the NTZ, revealing that predation was the main factor controlling the sea urchin populations inside the NTZ during the study period. Arbacia lixula reached the highest abundance and biomass values ever observed outside the NTZ in 2016. Our findings reveal that predation can control the establishment of new sea urchin populations and emphasize top-down control in NTZs, confirming the important role of fully protected areas in the structure of benthic communities.

Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae)

BACKGROUND

Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates.

RESULTS

We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species.

CONCLUSIONS

In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the species.

Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean

The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally. The main break corresponded to the separation of western Atlantic populations from those in eastern Atlantic and the Mediterranean Sea. A less marked, but significant differentiation was also found between Macaronesia (eastern Atlantic) and the Mediterranean. In the latter area, a signal of differentiation between the transitional area (Alboran Sea) and the rest of the Mediterranean was detected. However, no genetic structure is found within the Mediterranean (excluding Alboran) across the Siculo-Tunisian Strait, resulting from either enough gene flow to homogenize distance areas or/and a recent evolutionary history marked by demographic expansion in this basin. Genetic temporal variation at the Alboran Sea is as important as spatial variation, suggesting that temporal changes in hydrological features can affect the genetic composition of the populations. A picture of genetic homogeneity in the Mediterranean emerges, implying that the potential expansion of this keystone species will not be limited by intraspecific genetic features and/or potential impact of postulated barriers to gene flow in the region.

Early time course of variation in coelomic fluid ionic concentrations in sea urchins abruptly exposed to hypo- and hyper-osmotic salinity challenges: Role of size and cross-section area of test holes

Echinoderms are restricted to the marine environment and are osmoconformer invertebrates. However, some species live in unstable environments. Especially those species, and those of larger body size, tend to show variable, albeit transient, ionic gradients between their coelomic fluid and external seawater. In order to further examine how sea urchin size relates to apparent ionic permeability of their body wall/epithelia, specimens of Echinometra lucunter, Lytechinus variegatus, Paracentrotus gaimardi, and Arbacia lixula-A. lixula of two distinct populations, Rio de Janeiro and Santa Catarina-were abruptly transferred from 35 psu to either 25 or 45 psu. Sodium, chloride, magnesium, and potassium concentrations were assayed in their coelomic fluids after 0, 1, 2, and 3 hr of exposure. Relative area of putative permeable (i.e., cross section areas of soft tissues, or test holes) surfaces (PPS) was estimated in empty tests as the sum of the peristomial area (oral hole in the empty test) and the total cross-section area of ambulacral holes, divided by the total volume (TV) of the test. L. variegatus and E. lucunter, the largest species, had PPS/TV values similar to that of the much smaller P. gaimardi. A. lixula was the "most putatively-permeable and conformer" among them all, especially urchins from the Santa Catarina population. Internal ionic levels equilibrated faster with external water in 45 than in 25, and differences among ions were observed. Body size is relevant, among many other factors, to aid conformers such as sea urchins to dwell in intertidal unstable habitats.

Intraspecific genetic structure, divergence and high rates of clonality in an amphi-Atlantic starfish

Intraspecific genetic diversity and divergence have a large influence on the adaption and evolutionary potential of species. The widely distributed starfish, Coscinasterias tenuispina, combines sexual reproduction with asexual reproduction via fission. Here we analyse the phylogeography of this starfish to reveal historical and contemporary processes driving its intraspecific genetic divergence. We further consider whether asexual reproduction is the most important method of propagation throughout the distribution range of this species. Our study included 326 individuals from 16 populations, covering most of the species' distribution range. A total of 12 nuclear microsatellite loci and sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analysed. COI and microsatellites were clustered in two isolated lineages: one found along the southwestern Atlantic and the other along the northeastern Atlantic and Mediterranean Sea. This suggests the existence of two different evolutionary units. Marine barriers along the European coast would be responsible for population clustering: the Almeria-Oran Front that limits the entrance of migrants from the Atlantic to the Mediterranean, and the Siculo-Tunisian strait that divides the two Mediterranean basins. The presence of identical genotypes was detected in all populations, although two monoclonal populations were found in two sites where annual mean temperatures and minimum values were the lowest. Our results based on microsatellite loci showed that intrapopulation genetic diversity was significantly affected by clonality whereas it had lower effect for the global phylogeography of the species, although still some impact on populations' genetic divergence could be observed between some populations.

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.

Low genetic diversity and recent demographic expansion in the red starfish Echinaster sepositus (Retzius 1816)

Understanding the phylogeography and genetic structure of populations and the processes responsible of patterns therein is crucial for evaluating the vulnerability of marine species and developing management strategies. In this study, we explore how past climatic events and ongoing oceanographic and demographic processes have shaped the genetic structure and diversity of the Atlanto-Mediterranean red starfish Echinaster sepositus. The species is relatively abundant in some areas of the Mediterranean Sea, but some populations have dramatically decreased over recent years due to direct extraction for ornamental aquariums and souvenir industries. Analyses across most of the distribution range of the species based on the mitochondrial cytochrome c oxidase subunit I gene and eight microsatellite loci revealed very low intraspecific genetic diversity. The species showed a weak genetic structure within marine basins despite the a priori low dispersal potential of its lecithotrophic larva. Our results also revealed a very recent demographic expansion across the distribution range of the species. The genetic data presented here indicate that the species might be highly vulnerable, due to its low intraspecific genetic diversity.

Contrasted phylogeographic patterns on mitochondrial DNA of shallow and deep brittle stars across the Atlantic-Mediterranean area

Previous studies on Ophiothrix in European waters demonstrated the existence of two distinct species, Ophiothrix fragilis and Ophiothrix sp. II. Using phylogenetic and species delimitation techniques based on two mitochondrial genes (cytochrome c oxidase I and 16S rRNA) we prove the existence of a new congeneric species (Ophiothrix sp. III), occurring in the deep Atlantic coast of the Iberian Peninsula and the Alboran Sea. We compared phylogeographic patterns of these three Ophiothrix species to test whether closely related species are differentially affected by past demographic events and current oceanographic barriers. We used 432 sequences (137 of O. fragilis, 215 of Ophiothrix sp. II, and 80 of Ophiothrix sp. III) of the 16S rRNA from 23 Atlantic-Mediterranean locations for the analyses. We observed different geographic and bathymetric distributions, and contrasted phylogeography among species. Ophiothrix fragilis appeared genetically isolated between the Atlantic and Mediterranean basins, attributed to past vicariance during Pleistocene glaciations and a secondary contact associated to demographic expansion. This contrasts with the panmixia observed in Ophiothrix sp. II across the Atlantic-Mediterranean area. Results were not conclusive for Ophiothrix sp. III due to the lack of a more complete sampling within the Mediterranean Sea.

The invasive coral Oculina patagonica has not been recently introduced to the Mediterranean from the western Atlantic

Background

Effective policies, management, and scientific research programs depend on the correct identification of invasive species as being either native or introduced. However, many species continue to be misidentified. Oculina patagonica, first recorded in the Mediterranean Sea in 1966, is believed to have been introduced in anthropogenic times and expanding in a west to east direction. However, its present identification and status as a recently introduced species remain to be explored. In this study, we used multi-locus genetic data to test whether O. patagonica in the Mediterranean has been recently introduced from the western North Atlantic.

Results

We found no genetic or historical demographic evidence to support a recent introduction of O. patagonica from the western North Atlantic or an expansion across the Mediterranean. Instead, Mediterranean and Atlantic populations are genetically distinct and appear to have begun diverging about 5 Mya. We also found evidence of a fossil record of Oculina spp. existing in the eastern North Atlantic millions of years before the present.

Conclusions

Our results suggest that Mediterranean populations of O. patagonica have long been isolated from the western Atlantic, either in undetectable numbers or overlooked and undersampled sites and habitats, and have only recently been expanding to invasive levels as a result of environmental changes. Accurate identification of species’ invasive statuses will enable more effective research programs aimed at better understanding the mechanisms promoting the invasive nature of species, which can then lead to the implementation of efficient management plans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0356-7) contains supplementary material, which is available to authorized users.

Temperature modulates the response of the thermophilous sea urchin Arbacia lixula early life stages to CO2-driven acidification

The increasing abundances of the thermophilous black sea urchin Arbacia lixula in the Mediterranean Sea are attributed to the Western Mediterranean warming. However, few data are available on the potential impact of this warming on A. lixula in combination with other global stressors such as ocean acidification. The aim of this study is to investigate the interactive effects of increased temperature and of decreased pH on fertilization and early development of A. lixula. This was tested using a fully crossed design with four temperatures (20, 24, 26 and 27 °C) and two pH levels (pHNBS 8.2 and 7.9). Temperature and pH had no significant effect on fertilization and larval survival (2d) for temperature <27 °C. At 27 °C, the fertilization success was very low (<1%) and all larvae died within 2d. Both temperature and pH had effects on the developmental dynamics. Temperature appeared to modulate the impact of decreasing pH on the % of larvae reaching the pluteus stage leading to a positive effect (faster growth compared to pH 8.2) of low pH at 20 °C, a neutral effect at 24 °C and a negative effect (slower growth) at 26 °C. These results highlight the importance of considering a range of temperatures covering today and the future environmental variability in any experiment aiming at studying the impact of ocean acidification.