Assessment of coralline algal species diversity and composition at European CO₂ seeps using DNA barcoding

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Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

<p>Abstract</p> <p>Background</p> <p>The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.</p> <p>Results</p> <p>Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 10³to ca. 10⁴nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 10⁵nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches.</p> <p>Conclusions</p> <p>Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.</p

First freshwater coralline alga and the role of local features in a major biome transition

Coralline red algae are significant components of sea bottom and up to now considered as exclusively marine species. Here we presentthe first coralline alga from a freshwater environment, found in theCetina River (Adriatic Sea watershed).The alga is fully adapted to freshwater, as attested by reproductive structures, sporelings, and an inability to survive brackish conditions. Morphological and molecular phylogenetic analyses revealthe species belongs to Pneophyllum and is described as P. cetinaensis sp. nov.The marine-freshwatertransition most probably occurred during the last glaciation. The brackish-water ancestor was preadapted to osmotic stress and rapid changes in water salinity and temperature.The particular characteristics ofthe karst Cetina River, such as hard water enriched with dissolved calcium carbonate and a pH similarto the marine environment, favoured colonization ofthe river by a marine species.The upstream advance and dispersal is facilitated by exceptionally pronounced zoochory by freshwater gastropods. Pneophyllum cetinaensis defies the paradigm of Corallinales as an exclusively marine group

Flora coralinal no geniculada de la región macaronésica: evidencias moleculares de su singularidad y relaciones biogeográficas con la flora europea

XIX Simposio de Botánica Criptogámica, Las Palmas de Gran Canaria, 24-28 de junio de 2013.Después de las primeras contribuciones a la flora coralinal de la región macaronésica por parte de Lamarck (1815), Montagne (1840) y Viera (1868-1869), han sido unos pocos ficólogos los que han aportado nuevas especies para los diferentes archipiélagos que componen esta región (Foslie 1905, 1906, May 1912, Lemoine 1929). Aparte del componente endémico de su flora, otras especies citadas presentan una distribución mucho más amplia. En la flora coralinal de Canarias, Afonso-­Carrillo et al (1984) distinguieron cuatro grupos biogeográficos, dos de los cuales contienen especies citadas en las costas europeas mientras que otros dos corresponden a especies pantropicales y especies cosmopolitas, respectivamente. La contribución de especies europeas y tropicales también se hizo patente en un análisis global de las algas coralinas geniculadas presentes en esta región (Rosas-­Alquicira et al. 2011). Athanasiadis & Neto (2010) citaron Mesophyllum expansum para Azores e Islas Canarias, una especie característica del coralígeno mediterráneo. Los fondos de maërl fueron estudiados por Cabioch (1974) y Afonso-­Carrillo et al. (1982) en Madeira y Canarias. Las algas coralinas no geniculadas presentan una alta plasticidad fenotípica que conlleva tanto una variación extrema dentro de un mismo taxón como convergencias entre taxones filogenéticamente distantes (Steneck 1986) que lo convierte en un grupo taxonómicamente muy complejo. El reciente empleo de la taxonomía molecular en estas algas ha puesto de manifiesto la inestabilidad de ciertos caracteres morfológicos tradicionales y la existencia de especies crípticas (Bailey & Chapman 1998, Harvey et al. 2002, Vidal et al. 2003, Broom et al. 2008, Bittner et al. 2010, Le Gall et al. 2010, Hind & Saunders 2013). Desde 2011, se está llevando a cabo un estudio acerca de la diversidad de las algas coralinas no geniculadas de la costas europeas mediante el empleo de DNA barcoding. Para este proyecto, se han recogido unos 1500 especímenes en 128 localidades de la costas atlántica y mediterránea, desde el intermareal hasta 94 m de profundidad, incluyendo fondos de maërl y coralígeno. Adicionalmente, se han incluido diversas colecciones procedentes de Canarias y Madeira, así como algunos especímenes preservados en el herbario AZB de Azores. En el presente trabajo analizamos las relaciones biogeográficas entre ambas áreas de estudio basados en nuestras secuencias y en las existentes en las bases de datos BOLD y Genbank. Los resultados obtenidos aportan un mayor conocimiento de la flora coralinal macaronésica y sus particularidades florísticas

Invasion and MMP expression profile in desmoid tumours

Desmoid tumours are locally invasive soft tissue tumours in which beta-catenin mediated TCF-dependent transcription is activated. The role of soluble factors secreted by the myofibroblastic desmoid tumour, which could stimulate tumour invasiveness, was investigated. Using collagen gel invasion assays, the presence of factors stimulating invasion in desmoid conditioned media (CM) could be established. Since matrix metalloproteinases (MMPs) have been implicated in the process of tumoral invasion, the expression levels of the MMP family members were evaluated. Quantitative reverse transcription-PCR was used to determine the expression levels of MMP1, MMP2, MMP3, MMP7, MMP11, MMP12, MMP13, MMP14 and the inhibitors TIMP1, TIMP2 and TIMP3. Besides overexpression of MMP7, a known TCF-dependent target gene, a striking upregulation of the expression levels of MMP1, MMP3, MMP11, MMP12 and MMP13 in desmoid tumours, compared to unaffected fibroblasts from the same patients, was found. Treating the CM of desmoids with a synthetic and a physiologic MMP inhibitor reduced the invasion-stimulating capacity of the desmoid CM by approximately 50%. These results suggest the involvement of soluble factors, released by the desmoid cells, in stimulating invasion and implicate the MMPs as facilitators of invasion

First Early Hominin from Central Africa (Ishango, Democratic Republic of Congo)

Despite uncontested evidence for fossils belonging to the early hominin genus Australopithecus in East Africa from at least 4.2 million years ago (Ma), and from Chad by 3.5 Ma, thus far there has been no convincing evidence of Australopithecus, Paranthropus or early Homo from the western (Albertine) branch of the Rift Valley. Here we report the discovery of an isolated upper molar (#Ish25) from the Western Rift Valley site of Ishango in Central Africa in a derived context, overlying beds dated to between ca. 2.6 to 2.0 Ma. We used µCT imaging to compare its external and internal macro-morphology to upper molars of australopiths, and fossil and recent Homo. We show that the size and shape of the enamel-dentine junction (EDJ) surface discriminate between Plio-Pleistocene and post-Lower Pleistocene hominins, and that the Ishango molar clusters with australopiths and early Homo from East and southern Africa. A reassessment of the archaeological context of the specimen is consistent with the morphological evidence and suggest that early hominins were occupying this region by at least 2 Ma