Genotyping-by-sequencing: a promising tool for plant genetics research and breeding

YS Chung, SC Choi, TH Jun, C Kim - Horticulture, Environment, and …, 2017 - Springer
Plant genetics studies and breeding programs utilize the genetic variation caused by DNA
polymorphisms. Molecular makers are used to detect these variations in the DNA. The …

A new model army: Emerging fish models to study the genomics of vertebrate Evo‐Devo

I Braasch, SM Peterson, T Desvignes… - … Zoology Part B …, 2015 - Wiley Online Library
Many fields of biology—including vertebrate Evo‐Devo research—are facing an explosion of
genomic and transcriptomic sequence information and a multitude of fish species are now …

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 …

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

DAR Eaton - Bioinformatics, 2014 - academic.oup.com
Motivation: Restriction-site–associated genomic markers are a powerful tool for investigating
evolutionary questions at the population level, but are limited in their utility at deeper …

Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

A Mastretta‐Yanes, N Arrigo, N Alvarez… - Molecular ecology …, 2015 - Wiley Online Library
Restriction site‐associated DNA sequencing (RAD seq) provides researchers with the ability
to record genetic polymorphism across thousands of loci for nonmodel organisms …

Use of RAD sequencing for delimiting species

E Pante, J Abdelkrim, A Viricel, D Gey, SC France… - Heredity, 2015 - nature.com
RAD-tag sequencing is a promising method for conducting genome-wide evolutionary
studies. However, to date, only a handful of studies empirically tested its applicability above …

Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on collection specimens

T Suchan, C Pitteloud, NS Gerasimova, A Kostikova… - PloS one, 2016 - journals.plos.org
In the recent years, many protocols aimed at reproducibly sequencing reduced-genome
subsets in non-model organisms have been published. Among them, RAD-sequencing is …

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Z Baker, M Schumer, Y Haba, L Bashkirova, C Holland… - Elife, 2017 - elifesciences.org
Studies of highly diverged species have revealed two mechanisms by which meiotic
recombination is directed to the genome—through PRDM9 binding or by targeting promoter …

Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

K Du, JMB Ricci, Y Lu, M Garcia-Olazabal… - Nature …, 2024 - nature.com
Hybridization has been recognized to play important roles in evolution, however studies of
the genetic consequence are still lagging behind in vertebrates due to the lack of …

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

S Herrera, TM Shank - Molecular phylogenetics and evolution, 2016 - Elsevier
Species delimitations is problematic in many cases due to the difficulty of evaluating
predictions from species hypotheses. In many cases delimitations rely on subjective …