The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 x 10(-8)), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.Diabetes mellitus: pathophysiological changes and therap

Recent radiation of the Palmariaceae (rhodophyta)

Molecular phylogenetic studies on the evolution of the red algae indicate that this ancient division has many lineages that have recently undergone radiations. One such example is the cold-temperate family Palmariaceae. In this study, sequences from the ribosomal DNA internal transcribed spacer regions were compared among ten species in the Palmariaceae from both Atlantic and Pacific sites. Phylogenetic analyses of sequence data, in which Rhodophysema georgii Batters was used as outgroup and root, indicate a radiation into four clades, three of which contain species of ''Palmaria'' and the fourth species of Halosaccion. Palmaria palmata (L.) Kuntze, the type and only North Atlantic species in the genus, stands apart from all remaining species in the family and terminates the most basal branch in the rooted tree. The three more derived clades have radiated mainly in the North Pacific. Southern Ocean Palmaria and North Atlantic Devaleraea are hypothesized to have invaded from separate but closely related North Pacific ancestors. The ease with which sequences could be aligned combined with an unsaturated transition: transversion ratio and modest divergence involving predominantly point mutations suggests that the initial radiation is relatively recent (late Miocene-Pliocene) and that the Devaleraea-Palmaria clade is even more recent (late Pliocene-Pleistocene)

Postglacial recolonization and the biogeography of Palmaria mollis (Rhodophyta) along the Northeast Pacific coast

We used random amplified polymorphic DNA (RAPD) markers to examine the distribution of genotypes of Palmaria mollis (Setchell et Gardner) van der Meer et Bird, a red alga. We sampled populations along the Northeast Pacific coast from northern Washington to southwestern Alaska, an area extensively glaciated during the last ice age. Our objective was to determine whether the tracks of postglacial recolonization could be extracted from the extant pattern of genotype distribution in a species with limited dispersal capabilities. Thirty-eight individuals from 14 sites were sampled for RAPD markers using nine different random primers. As expected, individuals from the same population were more closely related to each other than to individuals from other populations. Relationships among populations, however, did not necessarily reflect geographic proximity. Rather, populations fell into groups corresponding approximately to outer and inner coastal sites: the northwestern end of Vancouver Island and the Queen Charlotte Islands formed one outer coast group, which associated with sites from Prince William Sound, the Alaska Peninsula, and Sitka, Alaska; the eastern side of Vancouver Island and Ketchikan, Alaska, represented one group of inner sites, which associated with sites near Juneau, Alaska and the eastern end of the Strait of Juan de Fuca. We conclude that this pattern does not represent a single postglacial recolonization event

Recent radiation of the Palmariaceae (rhodophyta)

Molecular phylogenetic studies on the evolution of the red algae indicate that this ancient division has many lineages that have recently undergone radiations. One such example is the cold-temperate family Palmariaceae. In this study, sequences from the ribosomal DNA internal transcribed spacer regions were compared among ten species in the Palmariaceae from both Atlantic and Pacific sites. Phylogenetic analyses of sequence data, in which Rhodophysema georgii Batters was used as outgroup and root, indicate a radiation into four clades, three of which contain species of ''Palmaria'' and the fourth species of Halosaccion. Palmaria palmata (L.) Kuntze, the type and only North Atlantic species in the genus, stands apart from all remaining species in the family and terminates the most basal branch in the rooted tree. The three more derived clades have radiated mainly in the North Pacific. Southern Ocean Palmaria and North Atlantic Devaleraea are hypothesized to have invaded from separate but closely related North Pacific ancestors. The ease with which sequences could be aligned combined with an unsaturated transition: transversion ratio and modest divergence involving predominantly point mutations suggests that the initial radiation is relatively recent (late Miocene-Pliocene) and that the Devaleraea-Palmaria clade is even more recent (late Pliocene-Pleistocene)

Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications

Marine macroalgae, especially the Rhodophyta, can be notoriously difficult to identify owing to their relatively simple morphology and anatomy, convergence, rampant phenotypic plasticity, and alternation of heteromorphic generations. It is thus not surprising that algal systematists have come to rely heavily on genetic tools for molecular assisted alpha taxonomy. Unfortunately the number of suitable marker systems in the three available genomes is enormous and, although most workers have settled on one of three or four models, the lack of an accepted standard hinders the comparison of results between laboratories. The advantages of a standard system are obvious for practical purposes of species discovery and identification; as well, compliance with a universal marker, such as cox1 being developed under the label ‘DNA barcode’, would allow algal systematists to benefit from the rapidly emerging technologies. Novel primers were developed for red algae to PCR amplify and sequence the 5′ cox1 ‘barcode’ region and were used to assess three known species-complex questions: (i) Mazzaella species in the Northeast Pacific; (ii) species of the genera Dilsea and Neodilsea in the Northeast Pacific; and (iii) Asteromenia peltata from three oceans. These models were selected because they have all caused confusion with regards to species number, distribution, and identification in the field, and because they have all been studied with molecular tools. In all cases the DNA barcode resolved accurately and unequivocally species identities and, with the enhanced sampling here, turned up a variety of novel observations in need of further taxonomic investigation