Patterns of colonization, evolution and gene flow in species of the genus Patella in the Macaronesian Islands

The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element

Satellite DNA (sat-DNA) was previously described as junk and selfish DNA in the cellular economy, without a clear functional role. However, during the last two decades, evidence has been accumulated about the roles of sat-DNA in different cellular functions and its probable involvement in tumorigenesis and adaptation to environmental changes. In molluscs, studies on sat-DNAs have been performed mainly on bivalve species, especially those of economic interest. Conversely, in Gastropoda (which includes about 80% of the currently described molluscs species), studies on sat-DNA have been largely neglected. In this study, we isolated and characterized a sat-DNA, here named PcH-sat, in the limpet Patella caerulea using the restriction enzyme method, particularly HaeIII. Monomeric units of PcH-sat are 179 bp long, AT-rich (58.7%), and with an identity among monomers ranging from 91.6 to 99.8%. Southern blot showed that PcH-sat is conserved in P. depressa and P. ulyssiponensis, while a smeared signal of hybridization was present in the other three investigated limpets (P. ferruginea, P. rustica and P. vulgata). Dot blot showed that PcH-sat represents about 10% of the genome of P. caerulea, 5% of that of P. depressa, and 0.3% of that of P. ulyssiponensis. FISH showed that PcH-sat was mainly localized on pericentromeric regions of chromosome pairs 2 and 4-7 of P. caerulea (2n = 18). A database search showed that PcH-sat contains a large segment (of 118 bp) showing high identity with a homologous trait of the Nin-SINE transposable element (TE) of the patellogastropod Lottia gigantea, supporting the hypothesis that TEs are involved in the rising and tandemization processes of sat-DNAs.

Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.

Evaluating the taxonomic status of the large sized Tricolia Risso, 1826 in the Northeast Atlantic and Mediterranean Sea

Despite a long history of taxonomic studies on the genus Tricolia Risso, 1826, there is a shortfall on thorough systematic molecular reviews of the taxon from the NE Atlantic and Mediterranean coasts. Aiming to assess the genetic distinctness among morphospecies and the taxonomic status of currently accepted large sized species in these areas, we conducted a molecular phylogenetic analysis of the genus based on one mitochondrial (cox1) and two nuclear (28S and ITS2) markers. Seven Tricolia species were consistently retrieved in the analyses, including a new genetic lineage in the NE Atlantic designated as Tricolia sp. 1. Molecular analyses revealed that only one species, T. azorica, occurs in the NE Atlantic archipelagos. The sister taxa T. pullus (Mediterranean) and T. picta (NE Atlantic) should be classified as distinct species, instead of subspecies of the T. pullus group (sensu Gofas 1982). Tricolia miniata is also a complex of species in the Mediterranean and future studies across the distribution range are necessary to clarify its status.

Genetic differentiation of a critically endangered population of the limpet Patella candei candei d’Orbigny, 1840, in the Canary Islands

The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d’Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecific relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically differentiated from the closely related P. candei crenata for the first time. Moreover, genetic differentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specific management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

Background

In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics.

Results

Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands.

Conclusions

Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01862-1.

Genetic diversity and population structure of the rockpool shrimp Palaemon elegans based on microsatellites: evidence for a cryptic species and differentiation across the Atlantic-Mediterranean transition

The rockpool shrimp Palaemon elegans is an ecologically important crustacean species within the European coastline fauna. In the present study, genetic diversity and population structure and connectivity were assessed by examining 21 polymorphic microsatellite loci at 13 sampling sites located along the natural distribution range. All localities showed similar levels of genetic variability. Significant deficits of heterozygosity were recorded, most likely due to the presence of null alleles. Genetic structure analyses revealed two clearly genetically distinct groups within P. elegans but without following any geographical or oceanographic basis. Thus, our results provided nuclear evidence for the existence of a Mediterranean cryptic species within P. elegans, highlighting the need to revise its taxonomic status. Regarding P. elegans sensu stricto, population structuring was reported across the Atlantic-Mediterranean transition area, where the Almería-Orán Front restricts the gene flow between the Atlantic and the Mediterranean population. Moreover, while population connectivity was suggested between all Mediterranean localities, some substructure was found within the Atlantic group. Canary Islands exhibited a weak but significant genetic differentiation from all Atlantic mainland localities, consistent with the isolation-by-distance pattern detected throughout the Atlantic population. Overall, all these findings provided new insights into the population biology of P. elegans complex.

Phylogeography of the insular populations of common octopus, Octopus vulgaris Cuvier, 1797, in the Atlantic Macaronesia

Exploited, understudied populations of the common octopus, Octopus vulgaris Cuvier, 1797, occur in the northeastern Atlantic (NEA) throughout Macaronesia, comprising the Azores, Madeira and Canaries, and also the Cabo Verde archipelago. This octopus species, found from the intertidal to shallow continental-shelf waters, is largely sedentary, and the subject of intense, frequently unregulated fishing effort. We infer connectivity among insular populations of this octopus. Mitochondrial control region and COX1 sequence datasets reveal two highly divergent haplogroups (α and β) at similar frequencies, with opposing clinal distributions along the sampled latitudinal range. Haplogroups have different demographic and phylogeographic patterns, with origins related to the two last glacial maxima. F_ST values suggest a significant differentiation for most pairwise comparisons, including insular and continental samples, from the Galicia and Morocco coasts, with the exception of pairwise comparisons for samples from Madeira and the Canaries populations. Results indicate the existence of genetically differentiated octopus populations throughout the NEA. This emphasizes the importance of regulations by autonomous regional governments of the Azores, Madeira and the Canaries, for appropriate management of insular octopus stocks.

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.

Genetic diversity and population structure of the blue jack mackerel Trachurus picturatus across its western distribution

Blue jack mackerel Trachurus picturatus collected at six sampling locations of the north-east Atlantic Ocean (Azores, Madeira, Canaries, and Matosinhos, Peniche and Portimão, mainland Portugal) and one location in the Mediterranean (Sicily), were used to examine the genetic structure of this species. Three mitochondrial gene regions (cytochrome c oxidase subunit I, cytochrome b and control region) were used to study the genetic structure of the species in Macaronesia, as well as to compare the genetic diversity of this region with published results from its eastern distribution. All markers indicated the absence of genetic structure among populations, with high indices of genetic diversity. These results suggest that the species went through a bottleneck event, followed by a recent population expansion. Moreover, the comparison with previously published results from the T. picturatus Mediterranean distribution suggests the existence of a single panmictic population throughout the species' full range. This was, however, an unexpected result since other methodologies have shown the presence of, at least, three different population-units in the NE Atlantic Ocean.

Disentangling the genetic and morphological structure of Patella candei complex in Macaronesia (NE Atlantic)

The uptake of natural living resources for human consumption has triggered serious changes in the balance of ecosystems. In the archipelagos of Macaronesia (NE Atlantic), limpets have been extensively exploited probably since islands were first colonized. This has led to profound consequences in the dynamics of rocky shore communities. The Patella candei complex includes various subspecies of limpets that are ascribed to a particular archipelago and has been the focus of several taxonomic surveys without much agreement. Under a conservational perspective, we apply morphometric and genetic analyses to test subspecies boundaries in P. candei and to evaluate its current population connectivity throughout Macaronesia (Azores, Madeira, and Canaries). A highly significant genetic break between archipelagos following isolation by distance was detected (F_ST = 0.369, p < .001). Contrastingly, significant genetic differentiation among islands (i.e., Azores) was absent possibly indicating ongoing gene flow via larval exchange between populations. Significant shell‐shape differences among archipelagos were also detected using both distance‐based and geometric morphometric analyses. Adaptive processes associated with niche differentiation and strong barriers to gene flow among archipelagos may be the mechanisms underlying P. candei diversification in Macaronesia. Under the very probable assumption that populations of P. candei from each archipelago are geographically and/or ecologically isolated populations, the various subspecies within the P. candei complex may be best thought of as true species using the denomination: P. candei in Selvagens, Patella gomesii in Azores, Patella ordinaria in Madeira, and Patella crenata for Canaries. This would be in agreement with stock delimitation and units of conservation of P. candei sensu latu along Macaronesia.

With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.

Mitochondrial DNA variability of the pipefish Syngnathus abaster

This study provides data on the genetic structuring of the pipefish Syngnathus abaster in the western Mediterranean and Adriatic Seas. A total of 109 specimens were collected in brackish-water biotopes. The control region and three other regions of the mitochondrial genome were analysed. The most relevant result was the high genetic structuring found by Bayesian inference (BI), maximum likelihood (ML) and network analyses, which were consistent in showing three well-separated clusters of S. abaster populations. Furthermore, BI and ML did not support the monophyly of the taxon S. abaster. These results suggest the occurrence of a species complex in the study area, whose differentiation may have occurred since the Pleistocene. The results also show a very high genetic variability at the inter-population level, with no shared haplotypes among sites. Evolutionary forces due to the fragmented nature of the brackish-water habitats may account for the high genetic divergence found among the groups and populations. Finally, although dispersal by rafting over long distances may occasionally occur, this study suggests linear stepping-stone model of colonization to be most likely. The complexity of the results obtained suggests that further studies are needed to elucidate the phylogeny of S. abaster.

Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean

Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.

Towards a model of postglacial biogeography in shallow marine species along the Patagonian Province: lessons from the limpet Nacella magellanica (Gmelin, 1791)

BACKGROUND

Patagonia extends for more than 84,000 km of irregular coasts is an area especially apt to evaluate how historic and contemporary processes influence the distribution and connectivity of shallow marine benthic organisms. The true limpet Nacella magellanica has a wide distribution in this province and represents a suitable model to infer the Quaternary glacial legacy on marine benthic organisms. This species inhabits ice-free rocky ecosystems, has a narrow bathymetric range and consequently should have been severely affected by recurrent glacial cycles during the Quaternary. We performed phylogeographic and demographic analyses of N. magellanica from 14 localities along its distribution in Pacific Patagonia, Atlantic Patagonia, and the Falkland/Malvinas Islands.

RESULTS

Mitochondrial (COI) DNA analyses of 357 individuals of N. magellanica revealed an absence of genetic differentiation in the species with a single genetic unit along Pacific Patagonia. However, we detected significant genetic differences among three main groups named Pacific Patagonia, Atlantic Patagonia and Falkland/Malvinas Islands. Migration rate estimations indicated asymmetrical gene flow, primarily from Pacific Patagonia to Atlantic Patagonia (Nem=2.21) and the Falkland/Malvinas Islands (Nem=16.6). Demographic reconstruction in Pacific Patagonia suggests a recent recolonization process (< 10 ka) supported by neutrality tests, mismatch distribution and the median-joining haplotype genealogy.

CONCLUSIONS

Absence of genetic structure, a single dominant haplotype, lack of correlation between geographic and genetic distance, high estimated migration rates and the signal of recent demographic growth represent a large body of evidence supporting the hypothesis of rapid postglacial expansion in this species in Pacific Patagonia. This expansion could have been sustained by larval dispersal following the main current system in this area. Lower levels of genetic diversity in inland sea areas suggest that fjords and channels represent the areas most recently colonized by the species. Hence recolonization seems to follow a west to east direction to areas that were progressively deglaciated. Significant genetic differences among Pacific, Atlantic and Falkland/Malvinas Islands populations may be also explained through disparities in their respective glaciological and geological histories. The Falkland/Malvinas Islands, more than representing a glacial refugium for the species, seems to constitute a sink area considering the strong asymmetric gene flow detected from Pacific to Atlantic sectors. These results suggest that historical and contemporary processes represent the main factors shaping the modern biogeography of most shallow marine benthic invertebrates inhabiting the Patagonian Province.

Patterns of spatial genetic structuring in the endangered limpet Patella ferruginea: implications for the conservation of a Mediterranean endemic

Patella ferruginea Gmelin, 1791 is an endangered marine gastropod endemic to the Western Mediterranean. Its range is restricted to the Sardinian-Corsican region (SCR), North Africa, a few scattered sites in Southern Spain, and Sicily. Inter-simple sequence repeat (ISSR) markers and three different mitochondrial DNA (mtDNA) regions, Cytochrome c Oxidase subunit I, 12S (small-subunit ribosomal RNA gene) and 16S (large-subunit ribosomal RNA gene), were used to investigate the presence of genetic population structuring. The mtDNA sequences showed very low levels of genetic differentiation. Conversely, ISSRs showed the presence of two main genetic groups, corresponding to Spain, North Africa and Sicily and the SCR. The SCR was further split into two subgroups. The ISSR results suggest that, on a regional scale, the genetic structure of P. ferruginea is mainly determined by the restriction of gene flow by dispersal barriers. On a more local scale human harvesting may play a crucial role in population structuring by increasing the effect of genetic drift.

Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea

Snails in the closely related trochid genera Phorcus Risso, 1826 and Osilinus Philippi, 1847 are ecologically important algal grazers in the intertidal zone of the northeastern Atlantic Ocean and Mediterranean Sea. Here we present the first complete molecular phylogeny for these genera, based on the nuclear 28S rRNA gene and the mitochondrial 16S rRNA and COI genes, and show that the current classification is erroneous. We recognize nine species in a single genus, Phorcus: estimated by BEAST analysis, this arose 30 (± 10) Ma; it consists of two subgenera, Phorcus and Osilinus, which we estimate diverged 14 (± 4.5) Ma. Osilinus kotschyi, from the Arabian and Red Seas, is not closely related and is tentatively referred to Priotrochus Fischer, 1879. Our phylogeny allows us to address biogeographical questions concerning the origins of the Mediterranean and Macaronesian species of this group. The former appear to have evolved from Atlantic ancestors that invaded the Mediterranean on several occasions after the Zanclean Flood, which ended the Messinian Salinity Crisis 5.3 Ma; whereas the latter arose from several colonizations of mainland Atlantic ancestors within the last 3 (± 1.5) Ma.

Phylogeography of the Atlanto-Mediterranean sea cucumber Holothuria (Holothuria) mammata: the combined effects of historical processes and current oceanographical pattern

We assessed the genetic structure of populations of the widely distributed sea cucumber Holothuria (Holothuria) mammata Grube, 1840, and investigated the effects of marine barriers to gene flow and historical processes. Several potential genetic breaks were considered, which would separate the Atlantic and Mediterranean basins, the isolated Macaronesian Islands from the other locations analysed, and the Western Mediterranean and Aegean Sea (Eastern Mediterranean). We analysed mitochondrial 16S and COI gene sequences from 177 individuals from four Atlantic locations and four Mediterranean locations. Haplotype diversity was high (H=0.9307 for 16S and 0.9203 for COI), and the haplotypes were closely related (π=0.0058 for 16S and 0.0071 for COI). The lowest genetic diversities were found in the Aegean Sea population. Our results showed that the COI gene was more variable and more useful for the detection of population structure than the 16S gene. The distribution of mtDNA haplotypes, the pairwise F(ST) values and the results of exact tests and amova revealed: (i) a significant genetic break between the population in the Aegean Sea and those in the other locations, as supported by both mitochondrial genes, and (ii) weak differentiation of the Canary and Azores Islands from the other populations; however, the populations from the Macaronesian Islands, Algarve and West Mediterranean could be considered to be a panmictic metapopulation. Isolation by distance was not identified in H. (H.) mammata. Historical events behind the observed findings, together with the current oceanographic patterns, were proposed and discussed as the main factors that determine the population structure and genetic signature of H. (H.) mammata.