A guide to carrying out a phylogenomic target sequence capture project

T Andermann, MF Torres Jiménez… - Frontiers in …, 2020 - frontiersin.org
High-throughput DNA sequencing techniques enable time-and cost-effective sequencing of
large portions of the genome. Instead of sequencing and annotating whole genomes, many …

aTRAM 2.0: an improved, flexible locus assembler for NGS data

JM Allen, R LaFrance, RA Folk… - Evolutionary …, 2018 - journals.sagepub.com
Massive strides have been made in technologies for collecting genome-scale data.
However, tools for efficiently and flexibly assembling raw outputs into downstream analytical …

Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

RA Folk, RL Stubbs, ME Mort… - Proceedings of the …, 2019 - National Acad Sciences
Environmental change can create opportunities for increased rates of lineage diversification,
but continued species accumulation has been hypothesized to lead to slowdowns via …

An integrated phylogenetic reassessment of the parasitoid superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) results in a revised familial classification

H Chen, Z Lahey, EJ Talamas, AA Valerio… - Systematic …, 2021 - Wiley Online Library
Abstract The superfamily Platygastroidea (Hymenoptera: Proctotrupomorpha) is a diverse
group of parasitoid wasps that are parasitoids of nine orders of insects as well as spiders …

Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)

LC Hughes, CM Nash, WT White… - Systematic …, 2023 - academic.oup.com
Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic
tree topologies for large species groups, help test the accuracy of and improve resolution for …

Phylogenomics of parasitic and nonparasitic lice (Insecta: Psocodea): combining sequence data and exploring compositional bias solutions in next generation data …

RS De Moya, K Yoshizawa, KKO Walden… - Systematic …, 2021 - academic.oup.com
The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and
nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group …

Phylogenomics from low‐coverage whole‐genome sequencing

F Zhang, Y Ding, CD Zhu, X Zhou… - Methods in Ecology …, 2019 - Wiley Online Library
Phylogenetic studies are increasingly reliant on next‐generation sequencing.
Transcriptomic and hybrid enrichment sequencing techniques remain the most prevalent …

Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution

R Allio, C Scornavacca, B Nabholz… - Systematic …, 2020 - academic.oup.com
Evolutionary relationships have remained unresolved in many well-studied groups, even
though advances in next-generation sequencing and analysis, using approaches such as …

Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes

EC Miller, R Faucher, PB Hart… - Nature Ecology & …, 2024 - nature.com
Colonization of a novel habitat is often followed by phenotypic diversification in the wake of
ecological opportunity. However, some habitats should be inherently more constraining than …

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

JK Olofsson, I Cantera, C Van de Paer… - Molecular ecology …, 2019 - Wiley Online Library
Species trees have traditionally been inferred from a few selected markers, and genome‐
wide investigations remain largely restricted to model organisms or small groups of species …