Applications of next-generation sequencing to phylogeography and phylogenetics.

By J. McCormack, S. Hird, A. Zellmer, Bryan C. Carstens, R. T. Brumfield. Molecular Phylogenetics and Evolution, 2013

638 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/648785153ba3fa59fab87af1d0ebb5cc4e3b00e1

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Citations in the corpus

Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera (2017, methodology): “Advances in sequencing technology and laboratory protocols have invigorated phylogenetic systematics (Lemmon & Lemmon 2013; McCormack et al. 2013b; Yeates et al. 2016).”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, background): “These approaches can be used to answer a wide variety of questions on population structure and phylogeography; see [51,53,57].”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Second, we present the phylogenetic data analysis workflow, with particular focus on the post-assembly steps, because recent reviews of primary sequence analysis, such as read assembly, already exist (e.g., Godden et al. 2012, McCormack et al. 2013).”
The new systematics of scleractinia: Integrating molecular and morphological evidence (2016, background): “These species tree methods have become especially relevant with the development of high-throughput sequencing technologies because it is now possible to generate orthologous sequence data in great abundance (McCormack et al. 2013).”
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).”
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics (2019, methodology): “More specifically, targeted enrichment or DNA sequence capture methods are becom - ing the gold standard in phylogenetic analyses because they allow subsampling the genome efficiently at reduced cost (Lemmon & Lemmon, 2013; McCormack et al., 2013).”
How to fail at species delimitation (2013, methodology): “Third, the field is no longer data limited, as advances in DNA sequencing allow data from 1000s of loci to be collected from nearly any system (McCormack et al. 2013).”
Higher level molecular phylogeny of darkling beetles (Coleoptera: Tenebrionidae) (2014, background): “E-mail: kergoat@supagro.inra.fr McCormack et al., 2013), the quest for a well-resolved and comprehensive tree of life remains ongoing (Drew, 2013).”
Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans‐Mexican Volcanic Belt (2015, background): “…high-resolution genomic data are increasingly becoming accessible and cost effective for phylogeographical and phylogenetic analyses (see McCormack et al., 2013 for a review), such as the sequencing of reduced representation libraries (e.g. Leach e et al., 2013; Mastretta-Yanes et al.,…”
Stacks: an analysis tool set for population genomics (2013, methodology): “Investigators have employed these methods to move from painstakingly developing dozens of microsatellite markers to rapidly producing tens of thousands of single nucleotide polymorphism (SNP) markers (Davey et al. 2011; McCormack et al. 2013).”
AMAS: a fast tool for alignment manipulation and computing of summary statistics (2016, neutral): “The amount of data used in modern phylogenetics has increased dramatically since the advent of nextgeneration sequencing (McCormack et al., 2013).”