Anchored hybrid enrichment for massively high-throughput phylogenomics.

By Alan R. Lemmon, Sandra A Emme, E. Lemmon. Systematic Biology, 2012

756 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ade500fdbe0eb6d4a51989db5988d0a92432a061

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Alan R. Lemmon
2. E. Lemmon
3. John J. Wiens
4. Jun Wen
5. Robert Lanfear
6. E. Zimmer
7. S. Winterton
8. B. Calcott

In Molecular Biology

1. Alan R. Lemmon
2. E. Lemmon
3. Jun Wen
4. John J. Wiens
5. Bin‐Bin Liu
6. Robert Lanfear
7. E. Zimmer
8. S. Winterton

In Plant Science

1. D. Ouvrard
2. Alan R. Lemmon
3. E. Lemmon
4. Diana M. Percy
5. John J. Wiens
6. F. Burbrink
7. R. Pyron
8. O. De Clerck

Citations in the corpus

• MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics (2019, background): “The field has witnessed the rapid parallel development of exon capture from transcriptome-de - rived baits (Bi et al., 2012), anchored hybrid enrichment techniques (Lemmon, Emme, & Lemmon, 2012), and the capture of ultraconserved DNA elements (UCEs; Faircloth et al., 2012).”
• DNA-based species delimitation in algae (2014, background): “Anchored hybrid enrichment or sequence capture is another development useful for producing large sets of nuclear loci across a wide range of samples (Lemmon et al., 2012), which will be highly informative about species boundaries (McCormack et al., 2013).”
• A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes (2013, methodology): “Next-generation sequencing strategies and phylogenomic methods should help resolve difficult nodes [16,20,36,198-200], as should application of species-tree methods [201,202].”
• The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, background): “…et al. 2012; Lemmon et al. 2012), among several others.”
• Selecting optimal partitioning schemes for phylogenomic datasets (2014, methodology): “However, recent reductions in DNA sequencing costs mean that it is now routine to produce very large ‘ phylogenomic ’ datasets which can contain hundreds or thousands of loci [23-25].”
• Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae (2021, background): “genome-scale methods developed to date, target enrichment, also known as Hyb-Seq, has been shown as the most efficient and cost-effective approach for obtaining large datasets of single-copy nuclear genes (SCNs) for plant systematics (Lemmon et al., 2012; Mandel et al., 2014; Weitemier et al., 2014;”
• Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera) (2018, methodology): “Extracted DNA was used to produce Illumina libraries following Lemmon et al. (2012) and Prum et al. (2015).”
• Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae) (2018, methodology): “Anchored Hybrid Enrichment (AHE) (Lemmon et al., 2012) is a relatively recent approach for hybrid enrichment that is now being used rather widely in phylogenomic studies of vertebrates (e.g. Brandley et al., 2015; Eytan et al., 2015; Prum et al., 2015) and most recently invertebrates (Diptera: Young”
• Resolving the psyllid tree of life: phylogenomic analyses of the superfamily Psylloidea (Hemiptera) (2018, methodology): “Library preparation and indexing were performed following a protocol modified from Meyer & Kircher (2010) (described in Lemmon et al., 2012).”
• Phylogenetic classification of bony fishes (2017, background): “, target enrichment [93, 94]), has ushered in a promising future to tackle difficult phylogenetic questions by analyzing hundreds or thousands of gene fragments [95].”
• Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture (2016, background): “This work adds to the growing literature illustrating the utility of targeted sequence capture for resolving relationships among species (Faircloth et al., 2012; Grover et al., 2012; Lemmon et al., 2012; McCormack et al., 2013; Weitemier et al., 2014), even within groups with low nucleotide substitu”
• A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, neutral): “See [112,113].”
• Species Delimitation: A Decade After the Renaissance (2013, neutral): “Decreasing se‐ quencing costs and new protocols for discovering and screening thousands of markers scattered throughout the genome [79], is now allowing application of population genomics approaches to identifying the candidate loci underlying adaptive traits with ecological sig‐ nificance [87].”
• Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches (2015, background): “…or “baits,” labeled with biotin for capture in solution, have become more often used, as microarray data production is more costly and less simple to work with and interpret (Cronn et al., 2012; Lemmon et al., 2012; Zhou & Holliday, 2012; Li et al., 2013; Stull et al., 2013; Stephens et al., 2015).”
• HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment (2016, background): “In one strategy, ultra-conserved elements can be used to anchor baits in slow-evolving portions of the genome, and analysis is focused on more variable flanking regions (Faircloth et al., 2012; Lemmon et al., 2012).”