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Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota
Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life…
HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment
…sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron…
Tectonic collision and uplift of Wallacea triggered the global songbird radiation
Songbirds originated in Australia and have now diversified into approximately 5,000 species found across the world. Here, Moyle et al. combine phylogenomic and biogeographic analyses to show that songbird diversification…
Target enrichment of thousands of ultraconserved elements sheds new light on early relationships within New World sparrows (Aves: Passerellidae)
Sparrows in the nine-primaried oscine family Passerellidae represent an attractive model for studying avian diversification across North and South America. However, the lack of phylogenetic resolution at the base of…
Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture
…genes in a crop, which might provide more durable resistance. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We…
Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga
Acropyga ants are a widespread clade of small subterranean formicines that live in obligate symbiotic associations with root mealybugs. We generated a data set of 944 loci of ultraconserved elements…
Differences in Homomorphic Sex Chromosomes Are Associated with Population Divergence in Sex Determination in Carinascincus ocellatus (Scincidae: Lygosominae)
Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains…
Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery
Premise of the study: We used moderately low-coverage (17×) whole-genome sequencing of Artocarpus camansi (Moraceae) to develop genomic resources for Artocarpus and Moraceae. Methods and Results: A de novo assembly…