Using genomic data to infer historic population dynamics of nonmodel organisms

AC Beichman, E Huerta-Sanchez… - Annual Review of …, 2018 - annualreviews.org
Genome sequence data are now being routinely obtained from many nonmodel organisms.
These data contain a wealth of information about the demographic history of the populations …

The utility of single nucleotide polymorphism (SNP) data in phylogenetics

AD Leaché, JR Oaks - Annual review of ecology, evolution, and …, 2017 - annualreviews.org
Resolving the genealogy of life—the phylogenetic relationships that describe the
evolutionary history of species—remains one of the great challenges of systematic biology …

Extreme elevational migration spurred cryptic speciation in giant hummingbirds

JL Williamson, EF Gyllenhaal, SM Bauernfeind… - Proceedings of the …, 2024 - pnas.org
The ecoevolutionary drivers of species niche expansion or contraction are critical for
biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation …

RAD capture (Rapture): flexible and efficient sequence-based genoty**

OA Ali, SM O'Rourke, SJ Amish, MH Meek, G Luikart… - Genetics, 2016 - academic.oup.com
Massively parallel sequencing has revolutionized many areas of biology, but sequencing
large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many …

Enriching the ant tree of life: enhanced UCE bait set for genome‐scale phylogenetics of ants and other Hymenoptera

MG Branstetter, JT Longino, PS Ward… - Methods in Ecology …, 2017 - Wiley Online Library
Targeted enrichment of conserved genomic regions (eg ultraconserved elements or UCEs)
has emerged as a promising tool for inferring evolutionary history in many organismal …

Misconceptions on missing data in RAD-seq phylogenetics with a deep-scale example from flowering plants

DAR Eaton, EL Spriggs, B Park… - Systematic …, 2017 - academic.oup.com
Restriction-site associated DNA (RAD) sequencing and related methods rely on the
conservation of enzyme recognition sites to isolate homologous DNA fragments for …

Phylogenomics using formalin‐fixed and 100+ year‐old intractable natural history specimens

S Ruane, CC Austin - Molecular ecology resources, 2017 - Wiley Online Library
Museum specimens provide a wealth of information to biologists, but obtaining genetic data
from formalin‐fixed and fluid‐preserved specimens remains challenging. While DNA …

An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives

PF Cowman, AM Quattrini, TCL Bridge… - Molecular Phylogenetics …, 2020 - Elsevier
Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution
of clades and inform taxonomy. Here, we redesign a custom bait set previously developed …

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

L Dietz, J Eberle, C Mayer, S Kukowka… - Methods in Ecology …, 2023 - Wiley Online Library
Species are the fundamental units of life and evolution. Their recognition is essential for
science and society. Molecular methods have been increasingly used for the identification of …

Identifying conserved genomic elements and designing universal bait sets to enrich them

BC Faircloth - Methods in Ecology and Evolution, 2017 - Wiley Online Library
Targeted enrichment of conserved genomic regions is a popular method for collecting large
amounts of sequence data from non‐model taxa for phylogenetic, phylogeographic and …