The origin of the European bison (Bison bonasus, Linnaeus, 1758) has been widely discussed and investigated in recent years. The species had a wide historic geographic distribution throughout the European continent during the middle and late Holocene, ranging from France in the west to the Caucasus in the east. However, archaeological evidence is needed to resolve the southern extent of the European bison distribution. We discovered one bison skull fragment during archaeological excavations in 2008 in the area of Yenikapı Metro and Marmaray (Turkey). Radiocarbon dating indicated the skull was deposited during the Byzantine period (seventh to eighth century AD). Mitochondrial genome analyses provided clear evidence that the skull was from a European bison. This is the first unambiguous evidence of the presence of this species in southeastern Europe during Byzantine times, which validates the historical written records of a potentially wider range of the European bison in historical times.

Wheat breeders and academics alike use Single Nucleotide Polymorphisms (SNPs) as molecular markers to characterise regions of interest within the hexaploid wheat genome. A number of SNP-based genotyping platforms are available and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated datasets. We predict that genotyping by sequencing will become the predominant genotyping technology within the next five to ten years. With this in mind, to ensure that data generated from current genotyping platforms continues to be of use, we have designed and utilised SNP-based capture probes from several thousand existing and publicly available probes from Axiom® and KASP™ genotyping platforms. We have validated our capture probes in a targeted genotyping by sequencing protocol using thirty one previously genotyped UK elite hexaploid wheat accessions. Data comparisons between targeted genotyping by sequencing, Axiom® array genotyping and KASP™ genotyping assays, identified a set of 3,256 probes which reliably bring together targeted genotyping by sequencing data with the previously available marker dataset. As such these probes are likely to be of considerable value to the wheat community. The probe details, full probe sequences and a custom built analysis pipeline may be freely downloaded from the CerealsDB. This article is protected by copyright. All rights reserved.

Today, next generation sequencing (NGS) is extensively used in the research setting. However, high costs of NGS testing still prevent its routine use in clinical practice. One of the factors affecting the cost of sequencing is the number of reads per site, i.e. the number of times each nucleotide gets sequenced. On the one hand, lower coverage makes the whole process much faster and less time-consuming. On the other hand, it results in poor data quality. No unanimous opinion has been reached yet as to what minimum depth of coverage can produce reliable results. The aim of this study was to determine the minimum number of reads sufficient for accurate base calling of heterozygous and single nucleotide variants (SNV). Using bioinformatics methods, we demonstrate that accuracy can be achieved at a minimum depth of 12X.

Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here, we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (~ 2200 species) that includes the cacti and harbors many evolutionary transitions to C$$_{mathrm{4}}$$ and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C$$_{mathrm{4}}$$ and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C$$_{mathrm{4}}$$ and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ~ 50% matrix completeness across data sets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae $$+$$ Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.