The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing ~20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of ~99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict first to fifth degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5000 SNP panel for forensic applications.

Abstract Genomic analysis of hybrid zones offers unique insights into emerging reproductive isolation and the dynamics of introgression. Because hybrid genomes consist of blocks inherited from one or the other parental taxon, linkage information is essential. In most cases, the spectrum of local ancestry tracts can be efficiently uncovered from dense linkage maps. Here, we report the development of such a map for the hybridizing toads, Bombina bombina and Bombina variegata (Anura: Bombinatoridae). Faced with the challenge of a large (7–10 Gb), repetitive genome, we set out to identify a large number of Mendelian markers in the nonrepetitive portion of the genome that report B. bombina vs B. variegata ancestry with appropriately quantified statistical support. Bait sequences for targeted enrichment were selected from a draft genome assembly, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Validation of the resulting map with 4755 markers underscored the large-scale synteny between Bombina and Xenopus tropicalis. By assessing the sex of late-stage F2 tadpoles from histological sections, we identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.

Resistance gene transcript enrichment sequencing (cDNA RenSeq) is a cost-effective method of discovering and quantifying NLR genes.

Hybridization capture is the most versatile technique for comprehensive, cost-effective sequencing of both viruses and bacteria in complex samples.

myBaits Custom RNA-Seq capture kits provide rapid, selective enrichment of target regions of interest from NGS libraries built from RNA samples.

The myBaits 16S-Hyb kit enriches the complete 16S rRNA locus, giving better taxonomic resolution compared to amplicon sequencing.

After nearly a decade of field inventories in which we preserved voucher specimens of the small terrestrial mammals of Sulawesi, we combined qualitative and quantitative analyses of morphological traits with molecular phylogenetics to better understand the diversity of shrews (Soricidae: Crocidura) on the island. We examined the morphology of 1368 specimens and obtained extensive molecular data from many of them, including mitochondrial DNA sequences from 851 specimens, up to five nuclear exons from 657 specimens, and thousands of ultraconserved elements from 90 specimens. By iteratively testing species limits using distinct character datasets and appropriate taxon sampling, we found clear, mostly consistent evidence for the existence of 21 species of shrews on Sulawesi, only seven of which were previously recognized. We divide these 21 species into five morphogroups, provide emended diagnoses of the seven previously named species, and describe 14 new species. The Long-Tailed Group contains Crocidura caudipilosa, C. elongata, C. microelongata, new species, and C. quasielongata, new species; the Rhoditis Group contains C. rhoditis, C. pseudorhoditis, new species, C. australis, new species, and C. pallida, new species; the Small-Bodied Group contains C. lea, C. levicula, C. baletei, new species, C. mediocris, new species, C. parva, new species, and C. tenebrosa, new species; the Thick-Tailed Group contains C. brevicauda, new species and C. caudicrassa, new species; and the Ordinary Group contains C. musseri, C. nigripes, C. normalis, new species, C. ordinaria, new species, and C. solita, new species. Documenting these endemic species reveals a local radiation (20 of the 21 species are members of an endemic clade) in which elevational gradients played a prominent role in either promoting speciation, or at a minimum, fostering the cooccurrence of phenotypically similar species. As now understood, the species-level diversity of Crocidura on Sulawesi is nearly three times the known diversity of any other insular shrew fauna. This study highlights the fact that if we wish to understand the true extent of biodiversity on Earth, large-scale, vouchered organismal inventories followed up with thorough examinations of genetic, morphological, and geographic traits are sorely needed in montane tropical regions, even for purportedly well-studied groups such as mammals.