Genotyping-by-sequencing: a promising tool for plant genetics research and breeding
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 …
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 …
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 …
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 …
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
Restriction site‐associated DNA sequencing (RAD seq) provides researchers with the ability
to record genetic polymorphism across thousands of loci for nonmodel organisms …
to record genetic polymorphism across thousands of loci for nonmodel organisms …
Use of RAD sequencing for delimiting species
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 …
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 …
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
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 …
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
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 …
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
Species delimitations is problematic in many cases due to the difficulty of evaluating
predictions from species hypotheses. In many cases delimitations rely on subjective …
predictions from species hypotheses. In many cases delimitations rely on subjective …