Aggregated Clumps of Lithistid Sponges: A Singular,Reef-Like Bathyal Habitat with Relevant Paleontological Connections

The advent of deep-sea exploration using video cameras has uncovered extensive sponge aggregations in virtually all oceans. Yet, a distinct type is herein reported from the Mediterranean: a monospecific reef-like formation built by the lithistid demosponge Leiodermatium pfeifferae. Erect, plate-like individuals (up to 80 cm) form bulky clumps, making up to 1.8 m high mounds (1.14 m on average) on the bottom, at a 760 m-deep seamount named SSS. The siliceous skeletal frameworks of the lithistids persist after sponge death, serving as a complex 3D substratum where new lithistids recruit, along with a varied fauna of other sessile and vagile organisms. The intricate aggregation of lithistid mounds functions as a “reef” formation, architecturally different from the archetypal "demosponge gardens" with disaggregating siliceous skeletons. Leiodermatium pfeifferae also occurred at two additional, close seamounts (EBJ and EBS), but, unlike at SSS, the isolated individuals never formed accretive clumps. The general oceanographic variables (temperature, salinity, dissolved nutrients, chlorophyll, and oxygen) revealed only minimal between-seamount differences, which cannot explain why sponge abundance at SSS is about two orders of magnitude higher than at EBJ or EBS. Large areas of the dense SSS aggregation were damaged, with detached and broken sponges and a few tangled fishing lines. Satellite vessel monitoring revealed low fishing activity around these seamounts. In contrast, international plans for gas and oil extraction at those locations raise serious concerns over the need for protecting urgently this unique, vulnerable habitat to avoid further alteration. Modern lithistids are a relict fauna from Jurassic and Cretaceous reefs and the roots of the very genus Leiodermatium can be traced back to those fossil formations. Therefore, understanding the causes behind the discovered lithistid aggregation is critical not only to its preservation, but also to elucidate how the extraordinary Mesozoic lithistid formations developed and functioned.     

Bees explain floral variation in a recent radiation of Linaria

The role of pollinators in floral divergence has long attracted the attention of evolutionary biologists. Although abundant studies have reported the effect of pollinators on flower‐shape variation and plant speciation, the influence of pollinators on plant species differentiation during rapid radiations and the specific consequences of shifts among similar pollinators are not well understood. Here, we evaluate the association between pollinators and floral morphology in a closely related and recently diversifying clade of Linaria species (sect. Supinae subsect. Supinae). Our approach combined pollinator observations, functional floral morphometric measures and phylogenetic comparative analyses. The fauna visiting Linaria species was determined by extensive surveys and categorized by a modularity algorithm, and the size and shape of flowers were analysed by means of standard and geometric morphometric measures. Standard measures failed to find relationships between the sizes of representative pollinators and flowers. However, discriminant function analyses of geometric morphometric data revealed that pollination niches are finer predictors of flower morphologies in Linaria if compared with phylogenetic relationships. Species with the most restrictive flowers displayed the most slender spurs and were pollinated by bees with larger proboscides. These restrictive flower shapes likely appeared more than once during the evolutionary history of the study group. We show that floral variation can be driven by shifts between pollinators that have been traditionally included in a single functional group, and discuss the consequences of such transitions for plant species differentiation during rapid radiations.     

Variation at interleukin-6 receptor gene is associated to joint damage in rheumatoid arthritis

IntroductionInterleukin-6 (IL-6) cytokine signaling is key in Rheumatoid Arthritis (RA) pathophysiology. Blocking IL-6 receptor (IL6R) has proven to be a highly effective treatment to prevent joint damage. This study was performed to investigate the association between the genetic variation at IL6R gene and the severity of joint damage in RA.MethodsIL6R gene tagging SNPs (n = 5) were genotyped in a discovery group of 527 RA patients from 5 different university hospitals from Spain. For each marker, a linear regression analysis was performed using an additive model and adjusting for the years of evolution of the disease, autoantibody status, gender and age. Haplotypes combining the SNPs were also estimated and tested for association with the level of joint destruction. Using an independent cohort of 705 RA patients from 6 university hospitals we performed a validation study of the SNPs associated in the discovery phase.ResultsIn the discovery group we found a highly significant association between IL6R SNP rs4845618 and the level of joint destruction in RA (P = 0.0058, P_corrected = 0.026), and a moderate association with SNP rs4453032 (P = 0.02, P_corrected = 0.05). The resulting haplotype from both SNPs was more significantly associated with joint damage (P = 0.0037, P_corrected = 0.011). Using the validation cohort, we replicated the association between the two IL-6R SNPs with the degree of joint destruction in RA (P = 0.007 and P = 0.04, meta-analysis P = 0.00011 and P = 0.0021, respectively), and the haplotype association (P = 0.0058, meta-analysis P = 6.64 e-5).ConclusionsGenetic variation at IL6R gene is associated with joint damage in RA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0737-8) contains supplementary material, which is available to authorized users.     

In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex

Some of the effects of past climate dynamics on plant and animal diversity make‐up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent‐based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein‐coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.     

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

We investigated DNA methylomes of pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles. Epigenetic alteration of B-ALLs occurred in two tracks: de novo methylation of small functional compartments and demethylation of large inter-compartmental backbones. The deviations were exaggerated in lamina-associated domains, with differences corresponding to methylation clusters and/or cytogenetic groups. Our data also suggested a pivotal role of polycomb and CTBP2 in de novo methylation, which may be traced back to bivalency status of embryonic stem cells. Driven by these potent epigenetic modulations, suppression of polycomb target genes was observed along with disruption of developmental fate and cell cycle and mismatch repair pathways and altered activities of key upstream regulators.