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Molecular identification of paleofeces from Bechan Cave, southeastern Utah, USA
…of the defecator, the preserved DNA is composed of a mixture of diverse microbial, floral and fungal constituents, with limited DNA from the host. However, in situations where skeletal remains…
Multilocus DNA barcoding – Species Identification with Multilocus Data
Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as…
Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements
…phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range…
17th Century Variola Virus Reveals the Recent History of Smallpox
…of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such…
Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing
…with single-molecule real-time (SMRT) sequencing (SMRT RenSeq) to clone Rpi-amr3i. This technology should enable de novo assembly of complete nucleotide-binding, leucine-rich repeat receptor (NLR) genes, their regulatory elements and complex…
Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens
…of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel…
Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences
The Cracidae (curassows, guans, and chachalacas) include some of the most spectacular and endangered Neotropical bird species. They lack a comprehensive phylogenetic hypothesis, hence their geographic origin and the history…
Sorting out relationships among the grouse and ptarmigan using intron, mitochondrial, and ultra-conserved element sequences
…rigorously, we then added over 3000 ultra-conserved element (UCE) loci (over 1.7 million bp) gathered using Illumina sequencing. The UCE topology agreed with that of the combined nuclear intron and…