Stacks: an analysis tool set for population genomics
The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
- J. Catchen, A. Amores, Paul A Hohenlohe, W. Cresko, J. Postlethwait
- BiologyG3: Genes, Genomes, Genetics
- 1 August 2011
The algorithms implemented in Stacks are reported and demonstrated to be efficacy by constructing loci from simulated RAD-tags taken from the stickleback reference genome and by recapitulating and improving a genetic map of the zebrafish, Danio rerio.
Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags
- Paul A Hohenlohe, S. Bassham, P. Etter, Nicholas Stiffler, Eric A. Johnson, W. Cresko
- BiologyPLoS Genetics
- 1 February 2010
Overall estimates of genetic diversity and differentiation among populations confirm the biogeographic hypothesis that large panmictic oceanic populations have repeatedly given rise to phenotypically divergent freshwater populations and identify several novel regions showing parallel differentiation across independent populations.
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
- J. Davey, Paul A Hohenlohe, P. Etter, J. Boone, J. Catchen, M. Blaxter
- BiologyNature reviews genetics
- 1 July 2011
Best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target.
Harnessing the power of RADseq for ecological and evolutionary genomics
- Kimberly R. Andrews, J. Good, M. Miller, G. Luikart, Paul A Hohenlohe
- BiologyNature reviews genetics
- 1 February 2016
This Review provides a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
Genomics and the future of conservation genetics
This work identifies and discusses those problems for which genomics will be most valuable for curbing the accelerating worldwide loss of biodiversity and provides guidance on whichgenomics tools and approaches will bemost appropriate to use for different aspects of conservation.
Genomics and the origin of species
Emergent trends and gaps in understanding are identified, new approaches to more fully integrate genomics into speciation research are proposed, and an integrative definition of the field of speciation genomics is provided.
Harnessing genomics for delineating conservation units.
Understanding The Evolution And Stability Of The G-Matrix
- S. J. Arnold, R. Bürger, Paul A Hohenlohe, Beverley C Ajie, A. Jones
- BiologyEvolution; international journal of organic…
- 1 October 2008
Simulation studies of evolving G-matrices offer solutions to some of the problems of stability and evolution of the G-Matrix, as well as a deeper, synthetic understanding of both theG-matrix and adaptive radiations.
Resolving postglacial phylogeography using high-throughput sequencing
- K. Emerson, C. Merz, C. Holzapfel
- BiologyProceedings of the National Academy of Sciences
- 26 August 2010
This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000–19,000 B.P.