Cerianthus lloydii (Ceriantharia: Anthozoa: Cnidaria): New Status and New Perspectives.

Subclass Ceriantharia is a well-defined and probably ancient group of marine benthic organisms renowned for their bilateral symmetry, which is reflected in the arrangement of tentacles and mesenteries. Four species of Ceriantharia have been reported in the Arctic, including Cerianthus lloydii Gosse, 1859, also known from the Northern Atlantic and Northern Pacific. The integrity of this species was questioned in the literature, so we performed a molecular study of C. lloydii from several geographically distant locations using 18S and COI genes. The phylogenetic reconstructions show that specimens of C. lloydii form a single group with high support (>0.98), subdivided into distinctive clades: (1) specimens from Northern Europe, the Black and Barents seas, and (2) specimens from the White, Kara, Laptev, and Bering seas and also the Canadian Arctic and the Labrador Sea available via the BOLD database. There are several BOLD COI sequences of Pachycerianthus borealis (Verrill, 1873), which form a third clade of the C. lloydii group, sister to the European and Arctic clades. Based on low similarity (COI 86-87%) between C. lloydii and the type species of the genus Cerianthus Delle Chiaje, 1841-C. membranaceus (Gmelin, 1791), we propose a new status for the genus Synarachnactis Carlgren, 1924, and a new family Synarachnactidae to accommodate C. lloydii.

Accurate fetal variant calling in the presence of maternal cell contamination.

High-throughput sequencing of fetal DNA is a promising and increasingly common method for the discovery of all (or all coding) genetic variants in the fetus, either as part of prenatal screening or diagnosis, or for genetic diagnosis of spontaneous abortions. In many cases, the fetal DNA (from chorionic villi, amniotic fluid, or abortive tissue) can be contaminated with maternal cells, resulting in the mixture of fetal and maternal DNA. This maternal cell contamination (MCC) undermines the assumption, made by traditional variant callers, that each allele in a heterozygous site is covered, on average, by 50% of the reads, and therefore can lead to erroneous genotype calls. We present a panel of methods for reducing the genotyping error in the presence of MCC. All methods start with the output of GATK HaplotypeCaller on the sequencing data for the (contaminated) fetal sample and both of its parents, and additionally rely on information about the MCC fraction (which itself is readily estimated from the high-throughput sequencing data). The first of these methods uses a Bayesian probabilistic model to correct the fetal genotype calls produced by MCC-unaware HaplotypeCaller. The other two methods "learn" the genotype-correction model from examples. We use simulated contaminated fetal data to train and test the models. Using the test sets, we show that all three methods lead to substantially improved accuracy when compared with the original MCC-unaware HaplotypeCaller calls. We then apply the best-performing method to three chorionic villus samples from spontaneously terminated pregnancies.

Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation.

Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.