Lost in parameter space: a road map for stacks

JR Paris, JR Stevens… - Methods in Ecology and …, 2017 - Wiley Online Library
Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted
method for genotyping populations of model and non‐model organisms. Generating a …

Molecular phylogenetics of snailfishes (Cottoidei: Liparidae) based on MtDNA and RADseq genomic analyses, with comments on selected morphological characters

JW Orr, I Spies, DE Stevenson, GC Longo, Y Kai… - Zootaxa, 2019 - biotaxa.org
Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis
of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c …

Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing

EN Wosula, W Chen, Z Fei… - Genome biology and …, 2017 - academic.oup.com
Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that
cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci …

Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

AG Rivera‐Colón, NC Rochette… - Molecular ecology …, 2021 - Wiley Online Library
Restriction‐site associated DNA sequencing (RADseq) has become a powerful and
versatile tool in modern population genomics, enabling large‐scale evolutionary and …

[HTML][HTML] How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

P Hühn, MS Dillenberger, M Gerschwitz-Eidt… - Molecular Phylogenetics …, 2022 - Elsevier
Analysing multiple genomic regions while incorporating detection and qualification of
discordance among regions has become standard for understanding phylogenetic …

Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails

T Hirano, T Saito, Y Tsunamoto, J Koseki, B Ye… - Scientific Reports, 2019 - nature.com
Phylogenetic incongruence has frequently been encountered among different molecular
markers. Recent progress in molecular phylogenomics has provided detailed and important …

Genotype‐free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

VM Warmuth, H Ellegren - Molecular Ecology Resources, 2019 - Wiley Online Library
Restriction‐site associated DNA sequencing (RADSeq) facilitates rapid generation of
thousands of genetic markers at relatively low cost; however, several sources of error …

Evolving in the darkness: phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity

T Mao, Y Liu, MM Vasconcellos, MR Pie… - Molecular Phylogenetics …, 2022 - Elsevier
Troglomorphism—any morphological adaptation enabling life to the constant darkness of
caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and …

Selected wildlife trematodes

MG Bolek, JT Detwiler, HA Stigge - Digenetic Trematodes, 2019 - Springer
The trematodes are a species-rich group of parasites, with some estimates suggesting that
there are more than 24,000 species. However, recent interests on the biology of trematodes …

Phylogeny, Taxonomy, and Biogeography of Pterocarya (Juglandaceae)

YG Song, Y Li, HH Meng, Y Fragnière, BJ Ge, H Sakio… - Plants, 2020 - mdpi.com
Relict species play an important role in understanding the biogeography of intercontinental
disjunctions. Pterocarya (a relict genus) is the valuable model taxon for studying the …