Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographical breaks in a Mediterranean endemic marine cave mysid

Distribution and Ecology of Decapod Crustaceans in Mediterranean Marine Caves: A Review

Decapod crustaceans are important components of the fauna of marine caves worldwide, yet information on their ecology is still scarce. Mediterranean marine caves are perhaps the best known of the world and may offer paradigms to the students of marine cave decapods from other geographic regions. This review summarizes and updates the existing knowledge about the decapod fauna of Mediterranean marine caves on the basis of a dataset of 76 species from 133 caves in 13 Mediterranean countries. Most species were found occasionally, while 15 species were comparatively frequent (found in at least seven caves). They comprise cryptobiotic and bathyphilic species that only secondarily colonize caves (secondary stygobiosis). Little is known about the population biology of cave decapods, and quantitative data are virtually lacking. The knowledge on Mediterranean marine cave decapods is far from being complete. Future research should focus on filling regional gaps and on the decapod ecological role: getting out at night to feed and resting in caves during daytime, decapods may import organic matter to the cave ecosystem. Some decapod species occurring in caves are protected by law. Ecological interest and the need for conservation initiatives combine to claim for intensifying research on the decapod fauna of the Mediterranean Sea caves.

Species Radiations in the Sea: What the Flock?

Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.

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.

At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri

The processes of vicariance and dispersal are central to our understanding of diversification, yet determining the factors that influence these processes remains a significant challenge in evolutionary biology. Caves offer ideal systems for examining the mechanisms underlying isolation, divergence, and speciation. Intrinsic ecological differences among cavernicolous organisms, such as the degree of cave dependence, are thought to be major factors influencing patterns of genetic isolation in caves. Using a comparative phylogeographic approach, we employed mitochondrial and nuclear markers to assess the evolutionary history of two ecologically distinct groups of terrestrial cave-dwelling springtails (Collembola) in the genera Pygmarrhopalites (Arrhopalitidae) and Pogonognathellus (Tomoceridae) that are codistributed in caves throughout the Salem Plateau-a once continuous karst region, now bisected by the Mississippi River Valley in Illinois and Missouri. Contrasting phylogeographic patterns recovered for troglobiotic Pygmarrhopalites sp. and eutroglophilic Pogonognathellus sp. suggests that obligate associations with cave habitats can restrict dispersal across major geographic barriers such as rivers and valleys, but may also facilitate subterranean dispersal between neighboring cave systems. Pygmarrhopalites sp. populations spanning the Mississippi River Valley were estimated to have diverged 2.9-4.8 Ma, which we attribute to vicariance resulting from climatic and geological processes involved in Mississippi River Valley formation beginning during the late Pliocene/early Pleistocene. Lastly, we conclude that the detection of many deeply divergent, morphologically cryptic, and microendemic lineages highlights our poor understanding of microarthropod diversity in caves and exposes potential conservation concerns.

A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.

Unexpected mosaic distribution of two hybridizing sibling lineages in the teleplanically dispersing snail Stramonita haemastoma suggests unusual postglacial redistribution or cryptic invasion

Molecular approaches have proven efficient to identify cryptic lineages within single taxonomic entities. Sometimes these cryptic lineages maybe previously unreported or unknown invasive taxa. The genetic structure of the marine gastropod Stramonita haemastoma has been examined in the Western Mediterranean and North‐Eastern Atlantic populations with mtDNA COI sequences and three newly developed microsatellite markers. We identified two cryptic lineages, differentially fixed for alternative mtDNA COI haplogroups and significantly differentiated at microsatellite loci. The mosaic distribution of the two lineages is unusual for a warm‐temperate marine invertebrate with a teleplanic larval stage. The Atlantic lineage was unexpectedly observed as a patch enclosed in the north of the Western Mediterranean Sea between eastern Spain and the French Riviera, and the Mediterranean lineage was found in Macronesian Islands. Although cyto‐nuclear disequilibrium is globally maintained, asymmetric introgression occurs in the Spanish region where the two lineages co‐occur in a hybrid zone. A first interpretation of our results is mito‐nuclear discordance in a stable postglacial hybrid zone. Under this hypothesis, though, the location of genetic discontinuities would be unusual among planktonic dispersers. An alternative interpretation is that the Atlantic lineage, also found in Senegal and Venezuela, has been introduced by human activities in the Mediterranean area and is introgressing Mediterranean genes during its propagation, as theoretically expected. This second hypothesis would add an additional example to the growing list of cryptic marine invasions revealed by molecular studies.

Phylogeographic structure, cryptic speciation and demographic history of the sharpbelly (Hemiculter leucisculus), a freshwater habitat generalist from southern China

BACKGROUND

Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species.

RESULTS

Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C). Lineages B and C showed a relatively narrower geographic distribution, whereas lineage A was widely distributed in numerous drainages. Divergence dates suggested that H. leucisculus populations diverged between 1.61-2.38 Ma. Bayesian species delimitation analysis using 12 nuclear DNA loci indicated the three lineages probably represented three valid taxa. Isolation-with-migration (IM) analysis found substantial gene flow has occurred among the three lineages. Demographic analyses showed that lineages B and C have experienced rapid demographic expansion at 0.03 Ma and 0.08 Ma, respectively.

CONCLUSIONS

Hemiculter leucisculus populations in drainages in southern China comprise three mtDNA lineages, and each of which may represent a separate species. Intense uplift of the Qinghai-Tibetan Plateau, evolution of Asian monsoons, changes in paleo-drainages, and poor dispersal ability may have driven the divergence of the three putative species. However, gene flow occurs among the three lineages. Climatic fluctuations have a prominent impact on the populations from the lineages B and C, but exerted little influence on the lineage A.

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.

Cryptic diversity, geographical endemism and allopolyploidy in NE Pacific seaweeds

Background

Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome. Here, using a congeneric phylogeographic approach, we investigated two monotypic and geographically complementary sister genera of north-east Pacific intertidal seaweeds (Hesperophycus and Pelvetiopsis), for which preliminary molecular tests revealed unexpected conflicts consistent with unrecognized cryptic diversity and hybridization.

Results

The three recovered mtDNA clades did not match a priori species delimitations. H. californicus was congruent, whereas widespread P. limitata encompassed two additional narrow-endemic species from California - P. arborescens (here genetically confirmed) and P. hybrida sp. nov. The congruence between the genotypic clusters and the mtDNA clades was absolute. Fixed heterozygosity was apparent in a high proportion of loci in P. limitata and P. hybrida, with genetic analyses showing that the latter was composed of both H. californicus and P. arborescens genomes. All four inferred species could be distinguished based on their general morphology.

Conclusions

This study confirmed additional diversity and reticulation within NE Pacific Hesperophycus/Pelvetiopsis, including the validity of the much endangered, modern climatic relict P. arborescens, and the identification of a new, stable allopolyploid species (P. hybrida) with clearly discernable ancestry (♀ H. californicus x ♂ P. arborescens), morphology, and geographical distribution. Allopolyploid speciation is otherwise completely unknown in brown seaweeds, and its unique occurrence within this genus (P. limitata possibly representing a second example) remains enigmatic. The taxonomic separation of Hesperophycus and Pelvetiopsis is not supported and the genera should be synonymized; we retain only the latter. The transitional coastline between Point Conception and Monterey Bay represented a diversity hotspot for the genus and the likely sites of extraordinary evolutionary events of allopolyploid speciation at sympatric range contact zones. This study pinpoints how much diversity (and evolutionary processes) potentially remains undiscovered even on a conspicuous seaweed genus from the well-studied Californian intertidal shores let alone in other, less studied marine groups and regions/depths.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0878-2) contains supplementary material, which is available to authorized users.

Mysida and Lophogastrida of Greece: a preliminary checklist

Background

The checklist of Mysida and Lophogastrida of Greece was created within the framework of the Greek Taxon Information System (GTIS), which is one of the applications of the LifeWatchGreece Research Infrastructure (ESFRI) resuming efforts to develop a complete checklist of species recorded and reported from Greek waters. The objectives of the present study were to update and cross-check taxonomically all records of Mysida and Lophogastrida species known to occur in Greek waters in order to search for inaccuracies and omissions.

New information

The up-to-date checklist of Mysida and Lophogastrida of Greece comprises 49 species, classified to 25 genera.