Dramatic loss of seagrass habitat under projected climate change in the Mediterranean Sea.

Although climate warming is affecting most marine ecosystems, the Mediterranean is showing earlier impacts. Foundation seagrasses are already experiencing a well-documented regression in the Mediterranean which could be aggravated by climate change. Here, we forecast distributions of two seagrasses and contrast predicted loss with discrete regions identified on the basis of extant genetic diversity. Under the worst-case scenario, Posidonia oceanica might lose 75% of suitable habitat by 2050 and is at risk of functional extinction by 2100, whereas Cymodocea nodosa would lose only 46.5% in that scenario as losses are compensated with gained and stable areas in the Atlantic. Besides, we predict that erosion of present genetic diversity and vicariant processes can happen, as all Mediterranean genetic regions could decrease considerably in extension in future warming scenarios. The functional extinction of Posidonia oceanica would have important ecological impacts and may also lead to the release of the massive carbon stocks these ecosystems stored over millennia.

A phylogeny and biogeographic analysis for the Cape-Pondweed family Aponogetonaceae (Alismatales).

The monocot family Aponogetonaceae (Alismatales) consists only of Aponogeton, with 57 species occurring in Africa, Madagascar, India and Sri Lanka, Southeast Asia and Australia. Earlier studies inferred a Madagascan or Australian origin for the genus. Aponogeton-like pollen is documented from the Late Cretaceous of Wyoming, the early mid-Eocene of Canada, and the late mid-Eocene of Greenland. We obtained nuclear and plastid DNA sequences for 42 species and generated a time-calibrated phylogeny, rooted on appropriate outgroups. Statistical biogeographic analyses were carried out with or without the fossils incorporated in the phylogeny. The recent-most common ancestor of living Aponogetonaceae appears to date to the mid-Eocene and to have lived in Madagascar or Africa (but not Australia). Three transoceanic dispersal events from Africa/Madagascar to Asia sometime during the Miocene could explain the observed species relationships. As inferred in earlier studies, an ancient Australian species is sister to all other Aponogetonaceae, while the remaining Australian species stem from an Asian ancestor that arrived about 5million years ago. The family's ancient Northern Hemisphere fossil record and deepest extant divergence between a single Australian species and an Africa/Madagascar clade are statistically well-supported and rank among the most unusual patters in the biogeography of flowering plants.

New highly polymorphic microsatellite markers for the aquatic angiosperm Ruppia cirrhosa reveal population diversity and differentiation.

Ruppia cirrhosa is a clonal monoecious plant phylogenetically associated to seagrass families such as Posidoniaceae and Cymodoceaceae. It inhabits shallow waters that are important for productivity and as a biodiversity reservoir. In this study, we developed 10 polymorphic microsatellite loci for R. cirrhosa. Additionally, we obtained cross-amplification for two microsatellites previously described for Ruppia maritima. These 12 markers were tested in four R. cirrhosa populations from the southwest of Europe. The number of alleles per locus was high for most of the markers, ranging from 4 to 13. Two populations (Sicily and Cádiz) showed heterozygote deficit (p < 0.001). The four populations (Sicily, Murcia, Cádiz, and Tavira) were significantly differentiated (F(ST) ≠ 0; p < 0.001), corroborating the usefulness of these microsatellites on R. cirrhosa population genetics.

Morphological and physiological responses of seagrasses (Alismatales) to grazers (Testudines: Cheloniidae) and the role of these responses as grazing patch abandonment cues.

Green sea turtles, Chelonia mydas, are grazers influencing the distribution of seagrass within shallow coastal ecosystems, yet the drivers behind C. mydas patch use within seagrass beds are largely unknown. Current theories center on food quality (nutrient content) as the plant responds to grazing disturbances; however, no study has monitored these parameters in a natural setting without grazer manipulation. To determine the morphological and physiological responses potentially influencing seagrass recovery from grazing disturbances, seagrasses were monitored for one year under three different grazing scenarios (turtle grazed, fish grazed and ungrazed) in a tropical ecosystem in Akumal Bay, Quintana Roo, Mexico. Significantly less soluble carbohydrates and increased nitrogen and phosphorus content in Thalassia testudinum were indicative of the stresses placed on seagrasses during herbivory. To determine if these physiological responses were the drivers of the heterogeneous grazing behavior by C. mydas recorded in Akumal Bay, patches were mapped and monitored over a six-month interval. The abandoned patches had the lowest standing crop rather than leaf nutrient or rhi- zome soluble carbohydrate content. This suggests a modified Giving Up Density (GUD) behavior: the critical threshold where cost of continued grazing does not provide minimum nutrients, therefore, new patches must be utilized, explains resource abandonment and mechanism behind C. mydas grazing. This study is the first to apply GUD theory, often applied in terrestrial literature, to explain marine herbivore grazing behavior.

Eurasian origin of Alismatidae inferred from statistical dispersal-vicariance analysis.

Alismatidae is a wetland or aquatic herb lineage of monocots with a cosmopolitan distribution. Although considerable progress in systematics and biogeography has been made in the past several decades, geographical origin of this group remains unresolved. In this study, we used statistical dispersal-vicariance analysis implemented in program RASP to investigate the biogeography of Alismatidae. Six areas of endemism were used to describe the distribution: North America, South America, Eurasia, Africa, Southeast Asia and Australia. 18,000 trees retained from Bayesian inference of rbcL served as a framework to reconstruct the ancestral areas. The results suggested that the most recent common ancestor of Alismatidae most probably occurred in Eurasia, followed by a split into two major clades. The clade comprising Hydrocharitaceae, Butomaceae and Alismataceae mainly diversified in Eurasia and Africa. The other clade comprising the remaining families dispersed to southern hemisphere. Australia played an important role in diversification of this clade. Several families were suggested to have occurred in Australia, such as Ruppiaceae, Cymodoceaceae, Posidoniaceae and Zosteraceae.

Comprehensive phylogenetic analyses of the Ruppia maritima complex focusing on taxa from the Mediterranean.

Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, "Drepanensis", was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former "Tetraploid" entity were reclassified into two entities: an Asia-Australia-Europe disjunct "Tetraploid_α" with a paternal "Diploid" origin, and a European "Tetraploid_γ" originating from a maternal "Drepanensis" lineage. Another entity, "Tetraploid_ß", is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal "Tetraploid_α" and maternal "Tetraploid_γ". Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia.

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life.

BACKGROUND: Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat. RESULTS: In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis. CONCLUSIONS: These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence.

Molecular phylogenetic analyses of Tofieldiaceae (Alismatales): family circumscription and intergeneric relationships.

Tofieldiaceae are a small monocot family comprising about 20 species, mostly distributed in the Northern Hemisphere, with some in northern South America. To clarify the family circumscription, the number of distinguishable genera in the family, and relationships among the genera, we conducted molecular analyses of cpDNA (matK and non-coding trnL-trnL-trnF region) sequences of 17 associated species of Tofieldiaceae, along with 14 species of Acorales, Alismatales, Dioscoreales, Pandanales, and Liliales. Results showed that Tofieldiaceae are monophyletic, comprising all the species assignable to Harperocallis, Isidrogalvia, Pleea, Tofieldia, and Triantha, thus supporting the original family circumscription. Within the family, Pleea is sister to the rest of the family, in which Isidrogalvia is sister to Harperocallis, and Tofieldia to Triantha. Morphological characters supporting the relationships among the genera were briefly discussed.

Network analysis identifies weak and strong links in a metapopulation system.

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system by using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and from the usual underlying hypotheses required for the interpretation of classical analyses, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial.

[Antioxidant effect and polyphenol content of Syringodium filiforme (Cymodoceaceae)]. / Efecto antioxidante y contenido polifenólico de Syringodium filiforme (Cymodoceaceae).

The marine phanerogam Syringodium filiforme, known as "manatee grass", is a common species that grows in coastal areas associated to Thalassia testudinum. With the aim to describe some of its possible chemical characteristics, this study was performed with a sample of 1.2 kg, collected in March 2009, in Guanabo beach, Havana, Cuba. The sample was dried (less than 12% humidity) and a total extract prepared; other three extracts were prepared with the use of solvents of increasing polarity. The phytochemical screening and analytical determinations of each fraction were undertaken Total polyphenol content was determined using pyrogallol as reference's standard; chlorophyll a and b and anthocyanin content were also quantified. Total extract and fractions antioxidant activity were evaluated by using the free radical scavenging activity assay with 1,1-Diphenyl-2-Picrylhydrazyl reactive (knowing as DPPH's method). The phytochemical screening of the different extracts detected the presence of high concentrations of flavonoids, phenols, terpenes, antocyanins, reducing sugars and alkaloids. The total extract and methanol fraction showed significant free radical scavenging properties, while the petroleum ether fraction showed moderate activity, and the chloroform fraction and the aqueous soluble precipitate (residual salt) obtained didn't show antioxidant properties against free radicals. The results of this work confirmed the potentialities of this species for biological purposes.

Impact of the Costa Concordia shipwreck on a Posidonia oceanica meadow: a multi-scale assessment from a population to a landscape level.

The Costa Concordia shipwreck permitted to assess how multiple disturbances affected marine biota at different spatial and temporal scales, evaluating the effects of mechanical and physical disturbances on Posidonia oceanica (L.) Delile, an endemic seagrass species of the Mediterranean Sea. To assess the impacts of the shipwreck and its salvaging from 2012 to 2017 at a population and a landscape level, a diversified approach was applied based on the application of a geographical information system coupled with seascape metrics and structural descriptors. Benthic habitat maps and seascape metrics highlighted cenotic transitions, as well as fragmentation and erosion phenomena, resulting in 9952 m2 of seagrass area impacted. Regression of the meadow was unveiled by both multivariate and interpolation analysis, revealing a clear spatio-temporal gradient of impacts based on distances from the wreck. Results highlighted the effectiveness of the descriptors involved that permitted to reveal temporal changes at both fine and large scales.

Spatial and temporal variations of meiofaunal communities from the western sector of the Gulf of Batabanó, Cuba: II. Seagrass systems.

The meiofauna from seagrass meadows in the western sector of the Gulf of Batabanó, Cuba were studied to describe the spatial and temporal variations in community structure. Replicated cores were taken in three locations (arranged in m- and km-scales) and in two seasons (dry and wet). The meiofauna (metazoans between 500 and 45 microm) were identified to major taxa. Temporal changes in the meiofaunal communities could not be detected and they are not linked to the subtle seasonal changes in the water column. A larger variation in community structure was observed in the spatial m-scale (among cores in a station) probably accredited to heterogeneity of microenvironment and biological processes. A second source of variation in the km-scale (among locations) was identified relating to physical processes affecting seagrass meadows: marine currents and anthropogenic disturbances. Distribution patterns of meiofauna across locations coincide with one study from 20 years ago in seagrass beds (i.e. higher densities in area closer to break-shelf and diminution of fauna at southern of Pinar del Rio); however, cumulative anthropogenic disturbances on seagrass meadows would most likely explain the depletion of communities observed in our survey in comparison with decades ago. Estimates of meiofaunal density and richness of major taxa from our study (and other areas from the Cuban shelf) are consistently lower than other temperate and tropical sites; possibly caused by low primary productivity due to narrow tidal amplitude and oligotrophic waters.

[Seagrass monitoring at Perezoso, Cahuita, Costa Rica (CARICOMP site)]. / Monitoreo de pastos marinos en Perezoso, Cahuita, Costa Rica (sitio CARICOMP).

The seagrass of Perezoso (Cahuita National Park, Caribbean coast of Costa Rica) was monitored using the CARICOMP protocol. Productivity (2.7 +/- 1.15 g/m2/d; n=74) was intermediate, compared to other Caribbean sites. Total biomass was intermediate to high (750-1500 g/m2) at most CARICOMP sites (Colombia, Cuba, Mexico, Puerto Rico and Venezuela) including Costa Rica (822.8 +/- 391.84 g/m2; n=32). Turnover rates were high (5.5 +/- 1.36%; n=74) compared to what was found in March and August at other sites. Shoot densities average 725 shoots/m2, in the Caribbean region, while in Costa Rica the value was higher (1184 +/- 335.5 shoots/m2). Average leaf length and width in the entire region were 14.4 cm and 10.6 mm, respectively, similar to what we found, but leaf area index average 3.4 m2 m(-2), higher than what was found in Costa Rica (0.92 m2 m(-2)). At Cahuita, seagrass productivity was significantly lower in March 2005 compared with the previous six years, and biomass has decreased with time. Seagrass productivity and biomass are being affected by the maximum temperatures, which increased by almost 10 degrees C from 1999 to 2005, and show a high negative correlation. Turnover rate and temperature were not correlated. Recreational boating, swimming and nutrient loading from deforested lands in the coast, the upstream rivers and local pollution are potential sources of impact to the seagrass beds at Cahuita.

[Does sea-grass biomass control the density of peracarids (Crustacea: Peracarida) in tropical lagoons?]. / Controla la biomasa de pastos marinos la densidad de los peracáridos (Crustacea: Peracarida) en lagunas tropicales?

We analyzed the time-space variation of the peracarid crustaceans that inhabit seagrasses of the Alvarado Lagoon System, Veracruz, Gulf of Mexico. The organisms were collected from 108 samples in six sites with Ruppia maritima beds (December 1992 to November 1994). The assemblage was composed of 11 species. Eight species of Amphipoda (Hourstonius laguna, Cerapus benthophilus, Apocorophium louisianum, Grandidierella bonnieroides, Leptocheirus rhizophorae, Gammarus mucronatus, Melita longisetosa and Haustorius sp.), one of Isopoda (Cassidinidea ovalis) and two of Tanaidacea (Discapseudes holthuisi and Leptochelia savignyi) were identified. Taxocoenosis, density and biomass of peracarids showed seasonal pulses related to R. maritima biomass, salinity variation, epicontinental affluent and inlets. The species C. ovalis, G. mucronatus, A. louisianum and D. holthuisi were dominant.

Seagrass meadows.

Seagrass meadows are an important and threatened ecosystem.

Palaeoclimatic conditions in the Mediterranean explain genetic diversity of Posidonia oceanica seagrass meadows.

Past environmental conditions in the Mediterranean Sea have been proposed as main drivers of the current patterns of distribution of genetic structure of the seagrass Posidonia oceanica, the foundation species of one of the most important ecosystems in the Mediterranean Sea. Yet, the location of cold climate refugia (persistence regions) for this species during the Last Glacial Maximum (LGM) is not clear, precluding the understanding of its biogeographical history. We used Ecological Niche Modelling together with existing phylogeographic data to locate Pleistocene refugia in the Mediterranean Sea and to develop a hypothetical past biogeographical distribution able to explain the genetic diversity presently found in P. oceanica meadows. To do that, we used an ensemble approach of six predictive algorithms and two Ocean General Circulation Models. The minimum SST in winter and the maximum SST in summer allowed us to hindcast the species range during the LGM. We found separate glacial refugia in each Mediterranean basin and in the Central region. Altogether, the results suggest that the Central region of the Mediterranean Sea was the most relevant cold climate refugium, supporting the hypothesis that long-term persistence there allowed the region to develop and retain its presently high proportion of the global genetic diversity of P. oceanica.

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.

Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales.

The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order:Potamogeton perfoliatus(Potamogetonaceae),Sagittaria lichuanensis(Alismataceae), andTofieldia thibetica(Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome ofS. lichuanensisis the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement. However, we detected 2.4 and 6 kb inversions in the plastid genomes ofSagittariaandPotamogeton, respectively. Further, we assembled a 79 plastid protein-coding gene sequence data matrix of 22 taxa that included the three newly generated plastid genomes plus 19 previously reported ones, which together represent all primary lineages of monocots and outgroups. In plastid phylogenomic analyses using maximum likelihood and Bayesian inference, we show both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales. More importantly, Tofieldiaceae was resolved as the most basal lineage within Alismatales. These results provide new insights into the evolution of Alismatales as well as the early-diverging monocots as a whole.

Nitrate fertilisation does not enhance CO2 responses in two tropical seagrass species.

Seagrasses are often considered "winners" of ocean acidification (OA); however, seagrass productivity responses to OA could be limited by nitrogen availability, since nitrogen-derived metabolites are required for carbon assimilation. We tested nitrogen uptake and assimilation, photosynthesis, growth, and carbon allocation responses of the tropical seagrasses Halodule uninervis and Thalassia hemprichii to OA scenarios (428, 734 and 1213 µatm pCO2) under two nutrients levels (0.3 and 1.9 µM NO3(-)). Net primary production (measured as oxygen production) and growth in H. uninervis increased with pCO2 enrichment, but were not affected by nitrate enrichment. However, nitrate enrichment reduced whole plant respiration in H. uninervis. Net primary production and growth did not show significant changes with pCO2 or nitrate by the end of the experiment (24 d) in T. hemprichii. However, nitrate incorporation in T. hemprichii was higher with nitrate enrichment. There was no evidence that nitrogen demand increased with pCO2 enrichment in either species. Contrary to our initial hypothesis, nutrient increases to levels approximating present day flood plumes only had small effects on metabolism. This study highlights that the paradigm of increased productivity of seagrasses under ocean acidification may not be valid for all species under all environmental conditions.

Biosystematic studies on the family Tofieldiaceae I. Phylogeny and circumscription of the family inferred from DNA sequences of matK and rbcL.

In order to specify phylogenetic positions of the genera of Tofieldiaceae (Tofieldia, Triantha, Pleea, Harperocallis, Isidrogalvia), and to suggest reasonable circumscription of the family and genera of Tofieldiaceae, we determined DNA sequences of matK and rbcL for each genus of the family, and analyzed them phylogenetically with the 45 families and 113 genera of the monocots other than Tofieldiaceae, whose matK and rbcL sequences have already been reported. We found that Tofieldia, Triantha, Pleea, and Harperocallis form the same clade, which receives 100% bootstrap support. This clade can be regarded as corresponding to Tofieldiaceae, and is embedded in the clade of Alismatales (98%). On the other hand, Isidrogalvia is not included in this Tofieldiaceae clade, and positioned as sister to Narthecium (100%), embedded in the clade of Nartheciaceae (Dioscoreales) (100%). In the Tofieldiaceae, Pleea first diverges from the remaining three genera (100%), and then, Harperocallis diverges from the Tofieldia- Triantha complex (100%). In the Tofieldia- Triantha complex, five Tofieldia species form the same clade (100%), and two Triantha species form another clade (100%). Thus, Isidrogalvia should be transferred from Tofieldiaceae to Nartheciaceae. As Isidrogalvia, as well as the Nartheciaceae, have the carpels that are fully connate into a single style, Isidrogalvia fits the Nartheciaceae well with respect to carpel connation. After this transfer, the Tofieldiaceae correspond mainly to plants with almost free carpels and three styles. Pleea is better treated as an independent genus than included in Tofieldia. Triantha can be treated either as an independent genus or as congeneric with Tofieldia.