European colonization by the spined loach (Cobitis taenia) from Ponto-Caspian refugia based on mitochondrial DNA variation

In the last 20 years, new species, asexual reproduction, polyploidy and hybridization have all been reported within the genus Cobitis. An understanding of the current distribution and baseline phylogeographical history of 'true' nonhybrid Cobitis species is crucial in order to unravel these discoveries. In the present work, we investigated the phylogeography of the spined loach, Cobitis taenia, using 1126 bp of the mitochondrial cytochrome b gene from 174 individuals collected at 47 sites. In total, 51 haplotypes that differed at 49 positions (4.35%) were detected. We deduce that C. taenia survived European glaciations in at least three refugees in the Ponto-Caspian area. Two of these refugees each provided a major lineage that recolonized Europe in separate directions: one westward to England and the other spreading north into Russia before moving west. A third (minor) lineage that contributed little to the recolonization of Europe was also revealed--remaining near its Black Sea refuge. However, more recent history was difficult to resolve with colonization from a more western refugium during the last glacial maximum (LGM) a distinct possibility. Nested clade analysis indicates a pattern of restricted gene flow with isolation by distance at the first two levels and overall. Unlike many other European freshwater fish species, the Danube is not part of the current distribution of C. taenia, nor was it used as either a refuge or a source of colonization of Europe. Low genetic diversity within C. taenia suggests that its colonization of Europe is relatively recent. Demographic analyses revealed a history of recent expansion and isolation by distance.     

High prevalence of cerebral venous sinus thrombosis (CVST) as presentation of cystathionine beta-synthase deficiency in childhood: Molecular and clinical findings of Turkish probands

Classical homocystinuria is the most commonly inherited disorder of sulfur metabolism, caused by the genetic alterations in human cystathionine beta-synthase (CBS) gene. In this study, we present comprehensive clinical findings and the genetic basis of homocystinuria in a cohort of Turkish patients. Excluding some CBS mutations, detailed genotype–phenotype correlation for different CBS mutations has not been established in literature. We aimed to make clinical subgroups according to main clinical symptoms and discussed these data together with mutational analysis results from our patients. Totally, 16 different mutations were identified; twelve of which had already been reported, and four are novel (p.N93Y, p.L251P, p.D281V and c.829−2A>T). The probands were classified into three major groups according to the clinical symptoms caused by these mutations. A psychomotor delay was the most common diagnostic symptom (n = 12, 46.2% neurological presentation), followed by thromboembolic events (n = 6, 23.1% vascular presentation) and lens ectopia, myopia or marfanoid features (n = 5, 19.2% connective tissue presentation). Pyridoxine responsiveness was 7.7%; however, with partial responsive probands, the ratio was 53.9%.     

Corrigendum

正Li W,Wang B,Wang M,Chen M,Yin JM,Kaleri GM,Zhang RJ,Zuo TN,You X and Yang Q(2014)Cloning and characterization of a potato StAN11gene involved in anthocyanin biosynthesis regulation.J Integr Plant Biol 56(4):364–372.DOI:10.1111/jipb.12136The authors would like to draw the reader’s attention to an error in the following article:     

Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade

Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094^T together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094^T was sequenced as part of the activities of the Transregional Collaborative Research Center 51 (TRR51) funded by the German Research Foundation (DFG).     

autoinfer1.0: a computer program to infer biogeographical events automatically

autoinfer is a computer program for biogeographical inference based on nested clade analysis. To reduce the obscurity caused by manual inference, we defined geographically concordant clades and intermediate geographical areas between two clades. The program will perform most of the inferences automatically with a minimum of input from the user. We believe that autoinfer will save much time for the user compared with using the inference key by hand and, furthermore, will reduce the errors of inference resulting from different criteria in deduction.     

Global database of plants with root‐symbiotic nitrogen fixation: NodDB

Plants associated with symbiotic N‐fixing bacteria play important roles in early successional, riparian and semi‐dry ecosystems. These so‐called N‐fixing plants are widely used for reclamation of disturbed vegetation and improvement of soil fertility in agroforestry. Yet, available information about plants that are capable of establishing nodulation is fragmented and somewhat outdated. This article introduces the NodDB database of N‐fixing plants based on morphological and phylogenetic evidence (available at https://doi.org/10.15156/bio/587469 ) and discusses plant groups with conflicting reports and interpretation, such as certain legume clades and the Zygophyllaceae family. During angiosperm evolution, N‐fixing plants became common in the fabid rather than in the ‘nitrogen‐fixing’ clade. The global GBIF plant species distribution data indicated that N‐fixing plants tend to be relatively more diverse in savanna and semi‐desert biomes. The compiled and re‐interpreted information about N‐fixing plants enables accurate analyses of biogeography and community ecology of biological N fixation.