Transcriptome sequences resolve deep relationships of the grape family

J Wen, Z Xiong, ZL Nie, L Mao, Y Zhu, XZ Kan… - PloS one, 2013 - journals.plos.org
Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep
relationships, thus impeding our understanding of the evolution of the family. Next …

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

A Riesgo, SCS Andrade, PP Sharma, M Novo… - Frontiers in …, 2012 - Springer
Introduction Traditionally, genomic or transcriptomic data have been restricted to a few
model or emerging model organisms, and to a handful of species of medical and/or …

A new orthology assessment method for phylogenomic data: unrooted phylogenetic orthology

JA Ballesteros, G Hormiga - Molecular Biology and Evolution, 2016 - academic.oup.com
Current sequencing technologies are making available unprecedented amounts of genetic
data for a large variety of species including nonmodel organisms. Although many …

Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological …

JM Hallas, TL Parchman, CR Feldman - Molecular Phylogenetics and …, 2022 - Elsevier
Garter snakes (Thamnophis) are a successful group of natricines endemic to North America.
They have become important natural models for ecological and evolutionary research, yet …

Unioverse: a phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida)

JM Pfeiffer, JW Breinholt, LM Page - Molecular Phylogenetics and …, 2019 - Elsevier
Freshwater mussels (order Unionoida) are a diverse radiation of parasitic bivalves that
require temporary larval encystment on vertebrate hosts to complete metamorphosis to free …

Sequence capture using PCR‐generated probes: A cost‐effective method of targeted high‐throughput sequencing for nonmodel organisms

JV Peñalba, LL Smith, MA Tonione… - Molecular ecology …, 2014 - Wiley Online Library
Recent advances in high‐throughput sequencing library preparation and subgenomic
enrichment methods have opened new avenues for population genetics and phylogenetics …

Black and white and read all over: the past, present and future of giant panda genetics

F Wei, Y Hu, L Zhu, MW Bruford, X Zhan… - Molecular …, 2012 - Wiley Online Library
Few species attract much more attention from the public and scientists than the giant panda
(A iluropoda melanoleuca), a popular, enigmatic but highly endangered species. The …

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

A Hejnol, CJ Lowe - … Transactions of the Royal Society B …, 2015 - royalsocietypublishing.org
Molecular biology has provided a rich dataset to develop hypotheses of nervous system
evolution. The startling patterning similarities between distantly related animals during the …

Analyzing contentious relationships and outlier genes in phylogenomics

JF Walker, JW Brown, SA Smith - Systematic biology, 2018 - academic.oup.com
Recent studies have demonstrated that conflict is common among gene trees in
phylogenomic studies, and that less than one percent of genes may ultimately drive species …

Exon-capture-based phylogeny and diversification of the venomous gastropods (Neogastropoda, Conoidea)

J Abdelkrim, L Aznar-Cormano… - Molecular Biology …, 2018 - academic.oup.com
Transcriptome-based exon capture methods provide an approach to recover several
hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep …