Surviving the Messinian Salinity Crisis? Divergence patterns in the genus Dendropoma (Gastropoda: Vermetidae) in the Mediterranean Sea

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.

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 connectivity of two marine gastropods in the Mediterranean Sea: seascape genetics reveals species-specific oceanographic drivers of gene flow

Oceanographic features such as currents, waves, temperature and salinity, together with life history traits, control patterns and rates of gene flow and contribute to shaping the population genetic structure of marine organisms. Seascape genetics is an emerging discipline that adopts a spatially explicit approach to examine biotic and abiotic factors that drive gene flow in marine environments. In this study, we examined factors that contribute to genetic differentiation in two coastal Mediterranean gastropods whose geographical ranges overlap but which inhabit different environments. The two species differ in several life history traits and in their dispersal capabilities. Genetic differentiation was relatively low for the trochid species Gibbula divaricata (F_ST  =0.059), and high for the vermetid species Dendropoma lebeche (F_ST  =0.410). Salinity emerged as the most important variable explaining the genetic structure of both species; sea surface temperature was also important for G. divaricata. For the more sessile D. lebeche, the coastline was predicted to provide important pathways for stepping-stone connectivity and gene flow. Our results provide a greater understanding of the factors influencing marine population connectivity, which may be useful to guide marine conservation and management in the Mediterranean.

Phylogeography of the mediterranean green seaweed Halimeda tuna (Ulvophyceae, Chlorophyta)

Populations of many Mediterranean marine species show a strong phylogeographic structure, but the knowledge available for native seaweeds is limited. We investigated the genetic diversity of the green alga Halimeda tuna based on two plastid markers (tufA gene and a newly developed amplicon spanning five ribosomal protein genes and intergenic spacers, the rpl2-rpl14 region). The tufA sequences showed that Mediterranean H. tuna represents a single, well-defined species. The rpl2-rpl14 results highlighted a genetic separation between western and eastern Mediterranean populations; specimens collected from widely scattered locations in the Adriatic/Ionian region shared a haplotype unique to this region, and formed a group separated from all western Mediterranean regions. Specimens from Sardinia also formed a unique haplotype. Within the western Mediterranean basin, a gradual shift in the frequency of haplotypes was apparent along a West-East gradient. Our results represent the first clear evidence of an East-West genetic cleavage in a native Mediterranean macroalga and offer an interesting perspective for further research into fine-scale seaweed population structure in the NW Mediterranean Sea.

Phylogeography of Dictyota fasciola and Dictyota mediterranea (Dictyotales, Phaeophyceae): unexpected patterns on the Atlantic-Mediterranean marine transition and taxonomic implications

The Atlantic-Mediterranean marine transition is a fascinating biogeographic region, but still very poorly studied from the point of view of seaweed phylogeography. Dictyota fasciola and D. mediterranea (Dictyotales, Phaeophyceae) are two currently recognized sister species that share a large part of their distribution along the Mediterranean Sea and the Atlantic Ocean, representing a unique study model to understand the diversification processes experienced by macroalgae during and after Messinian at this marine region. In this study, we sampled 102 individuals of D. fasciola and D. mediterranea from 32 localities along their distribution range and sequenced the mitochondrial cox1 and the chloroplast rbcL-rbcS DNA regions for all the samples. Our data do not support the occurrence of two sister species but a morphologically variable and highly genetic diverse species or a complex of species. Most of the observed genetic diversity corresponds to the Mediterranean populations, whereas the Atlantic ones are much more homogeneous. The early-diverged lineages inferred from both mtDNA and cpDNA phylogenetic reconstructions were constituted by samples from the Mediterranean Sea. Together, these results suggest that the Mediterranean Sea acted as a refugium for the D. fasciola–D. mediterranea lineage during the geologic and climatic changes occurred on the region since the Miocene, subsequently dispersing to the Atlantic Ocean.

Mediterranean Lithophyllum stictiforme (Corallinales, Rhodophyta) is a genetically diverse species complex: implications for species circumscription, biogeography and conservation of coralligenous habitats

Lithophyllum species in the Mediterranean Sea function as algal bioconstructors, contributing to the formation of biogenic habitats such as coralligenous concretions. In such habitats, thalli of Lithophyllum, consisting of crusts or lamellae with entire or lobed margins, have been variously referred to as either one species, L. stictiforme, or two species, L. stictiforme and L. cabiochiae, in the recent literature. We investigated species diversity and phylogenetic relationships in these algae by sequencing three markers (psbA and rbcL genes, cox2,3 spacer), in conjunction with methods for algorithmic delimitation of species (ABGD and GMYC). Mediterranean subtidal Lithophyllum belong to a well-supported lineage, hereby called the L. stictiforme complex, which also includes two species described from the Atlantic, L. lobatum and L. searlesii. Our results indicate that the L. stictiforme complex consists of at least 13 species. Among the Mediterranean species, some are widely distributed and span most of the western and central Mediterranean, whereas others appear to be restricted to specific localities. These patterns are interpreted as possibly resulting from allopatric speciation events that took place during the Messinian Salinity Crisis and subsequent glacial periods. A partial rbcL sequence from the lectotype of L. stictiforme unambiguously indicates that this name applies to the most common subtidal Lithophyllum in the central Mediterranean. We agree with recent treatments that considered L. cabiochiae and L. stictiforme conspecific. The diversity of Lithophyllum in Mediterranean coralligenous habitats has been substantially underestimated, and future work on these and other Mediterranean corallines should use identifications based on DNA sequences.

Isolation of microsatellite loci for the endangered vermetid gastropod Dendropoma lebeche using Illumina MiSeq next generation sequencing technology

Dendropoma petraeum, considered the primary vermetid reef-building species in the Mediterranean, has recently been shown to be a species complex of at least four cryptic species. These species have highly restricted, non-overlapping distributions, causing concern for their conservation status. To better study the genetic diversity of these populations, we selected one of these species, Dendropoma lebeche (Templado et al. in Mediterr Mar Sci 17(1):13-31, 2016), which is restricted to the western Mediterranean, for microsatellite marker development using Illumina MiSeq. We provide an initial survey of 29 polymorphic microsatellite loci for D. lebeche. Genetic analyses identified 2-11 alleles per locus across the 30 samples examined. Observed and expected heterozygosities ranged from 0.067 to 0.800 and 0.064 to 0.770, respectively. None of the loci deviated from Hardy-Weinberg equilibrium or showed signs of being under selective pressure. Significant linkage disequilibrium was found between two loci. We also show the cross-species amplification of these microsatellite markers in the other three species of the complex, the Tyrrhenian-Sicilian lineage, D. cristatum (Biondi, 1859), the Levantine lineage, D. anguliferum (Monterosato, 1878) and Dendropoma sp. found along the Ionian-Aegean coasts, suggesting their potential utility for future phylogenetic and evolutionary studies.

Settlement performance of the Mediterranean reef-builders Dendropoma cristatum (Biondi 1859) in response to natural bacterial films

The gastropod Dendropoma cristatum is a biogenic engineer of the central Mediterranean, forming reefs along the lower rocky intertidal fringe with a remarkable ecological role. To understand whether reef-associated biofilm cultivable bacterial and biofilm ageing may trigger the settlement of the juvenile snails, a combination of laboratory techniques and field experiments was used. Reef-associated biofilm cultivable bacteria were isolated, and a settlement-choice experiment was performed in situ on artificial biofilms composed of i) a mixture of six biofilm-forming selected isolates, ii) all the cultivable bacteria, and iii) 13-, 23-, 32-day old biofilms formed under natural conditions. Overall, settlement rate significantly differed among biofilm treatments (p < 0.0001). A significant positive correlation between biofilm ageing and juvenile D. cristatum settlement was assessed (r = 0.69 (p < 0.001), whereas the biofilm bacterial composition (relatively to the cultivable fraction) did not show any effect on the vermetid's settlement rate.

Global biogeography, cryptic species and systematic issues in the shrimp genus Hippolyte Leach, 1814 (Decapoda: Caridea: Hippolytidae) by multimarker analyses

Hippolyte is a genus of small bodied marine shrimps, with a global distribution. Here, we studied the phylogenetic and biogeographic relationships amongst the species of this genus with two mitochondrial and two nuclear markers, using Bayesian Inference, Maximum Likelihood, genetic divergence, molecular clock and S-DIVA. In addition, the Indo-West Pacific genus Alcyonohippolyte was included. Based on sequences from 57 specimens of 27 species, we recovered a robust biogeographic scenario that shows the Indo-West Pacific as the probable ancestral area of the genus Hippolyte, which emerged in the Paleocene, followed by dispersal in three general directions: (1) South Pacific, (2) eastern Atlantic and Mediterranean Sea and (3) Americas, the latter with a primary colonization in the eastern Pacific followed by a radiation into the western Atlantic. Our analysis reveals that the species of the H. ventricosa group do not constitute a monophyletic group and Alcyonohippolyte does not constitute a reciprocally monophyletic group to Hippolyte, with both genera herein synonimised. The relationships and systematic status of several transisthmian and Atlantic species are clarified.

Genetic and morphological variation in an ecosystem engineer, Lithophyllum byssoides (Corallinales, Rhodophyta)

Lithophyllum byssoides is a common coralline alga in the intertidal zone of Mediterranean coasts, where it produces biogenic concretions housing a high algal and invertebrate biodiversity. This species is an ecosystem engineer and is considered a target for conservation efforts, but designing effective conservation strategies currently is impossible due to lack of information about its population structure. The morphological and molecular variation of L. byssoides was investigated using morphoanatomy and DNA sequences (psbA and cox2,3) obtained from populations at 15 localities on the Italian and Croatian coasts. Lithophyllum byssoides exhibited a high number of haplotypes (31 psbA haplotypes and 24 cox2,3 haplotypes) in the central Mediterranean. The psbA and cox2,3 phylogenies were congruent and showed seven lineages. For most of these clades, the distribution was limited to one or a few localities, but one of them (clade 7) was widespread across the central Mediterranean, spanning the main biogeographic boundaries recognized in this area. The central Mediterranean populations formed a lineage separate from Atlantic samples; psbA pair-wise divergences suggested that recognition of Atlantic and Mediterranean L. byssoides as different species may be appropriate. The central Mediterranean haplotype patterns of L. byssoides were interpreted as resulting from past climatic events in the hydrogeological history of the Mediterranean Sea. The high haplotype diversity and the restricted spatial distribution of the seven lineages suggest that individual populations should be managed as independent units.

Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages?

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.

Multi-species collapses at the warm edge of a warming sea

Even during the current biodiversity crisis, reports on population collapses of highly abundant, non-harvested marine species were rare until very recently. This is starting to change, especially at the warm edge of species’ distributions where populations are more vulnerable to stress. The Levant basin is the southeastern edge of distribution of most Mediterranean species. Coastal water conditions are naturally extreme, and are fast warming, making it a potential hotspot for species collapses. Using multiple data sources, I found strong evidence for major, sustained, population collapses of two urchins, one large predatory gastropod and a reef-building gastropod. Furthermore, of 59 molluscan species once-described in the taxonomic literature as common on Levant reefs, 38 were not found in the present-day surveys, and there was a total domination of non-indigenous species in molluscan assemblages. Temperature trends indicate an exceptional warming of the coastal waters in the past three decades. Though speculative at this stage, the fast rise in SST may have helped pushing these invertebrates beyond their physiological tolerance limits leading to population collapses and possible extirpations. If so, these collapses may indicate the initiation of a multi-species range contraction at the Mediterranean southeastern edge that may spread westward with additional warming.