Applications
Phylogenetics

In order to fully understand the evolutionary development of a gene, population, or species, it is critical to have accurate sequencing data.

The power and scale of Next-Generation Sequencing (NGS) provides the necessary sequencing depth for phylogenetic analysis and pairing with target capture technology can greatly increase discovery. The flexible nature of hybridization-based target capture technology can tolerate multiple nucleotide sequence mismatches between the synthetic capture probe and the target NGS library molecule. This simple yet critical principle has turned NGS-based sequence capture into one of the most significant and powerful tools for variant discovery, evolutionary, and phylogenetic research.

Hybridization-based target capture is perfect for recovering unknown variation on the scale of hundreds, thousands, or even tens of thousands of genomic loci, which is ideal for high-resolution phylogenetics among both closely- and distantly-related individuals. Critically, it also allows the use of related species reference sequences to be used for probe design when capturing various taxa. As the number of sequenced genomes and transcriptomes increase daily, evolutionary relationships between almost any group of non-model organisms can now be studied with the help of NGS target capture technology.

Unlike other genotyping technologies which are rigid or require large upfront orders to reach feasible per-sample costs, myBaits Custom target capture kits are highly flexible and scalable for any size project. Sequencing hundreds or thousands of samples and loci at once becomes feasible within a wide range of research budgets. The experienced scientists at Arbor Biosciences will work directly with you to choose the correct product and bait set for your phylogenetic research project. Our popular line of myBaits target capture kits, including custom panels, ultraconserved elements, mitochondrial DNA sequencing, and more are compatible with any size phylogenetic project and research budget.

 

Featured Publications

O.A. Ali et al. (2016). RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. Genetics

E.M. Gardner et al. (2016). Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery. Applications in Plant Sciences

M.G. Johnson et al. (2016). HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment. Applications in Plant Sciences

H.B. Shaffer et al. (2017). Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Molecular Phylogenetics and Evolution

S. Singhal et al. (2017). Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Molecular Ecology Resources

C. Li et al. (2017). Capturing protein-coding genes across highly divergent species. BioTechniques

B.C. Faircloth et al. (2012). Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Systematic Biology

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