Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
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TLDR
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.Abstract:
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. 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.read more
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Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
Gianpiero Marconi,Stefano Capomaccio,Cinzia Comino,Alberto Acquadro,Ezio Portis,Andrea Porceddu,Emidio Albertini +6 more
TL;DR: The methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd) is described, a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6 mA).
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Insights from a general, full‐likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging
TL;DR: A full‐likelihood Bayesian method is introduced that uses genomic data to estimate temporal clustering of an arbitrary mix of population divergences and population‐size changes across taxa and finds that estimating the timing and sharing of demographic changes tends to be inaccurate and sensitive to prior assumptions.
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Genomic insights into hybridization in a localized region of sympatry between pewee sister species (Contopus sordidulus × C. virens) and their chromosomal patterns of differentiation
TL;DR: The first conclusive evidence of hybridization between C.sordidulus and C. virens is provided in a region where secondary contact likely occurred due to human disturbance and habitat modification and the genomic patterns of differentiation affirm that these species split in the relatively recent past.
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Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes.
Sara Lado,Jean P. Elbers,Angela Doskocil,Davide Scaglione,Emiliano Trucchi,Mohammad Hossein Banabazi,Faisal Almathen,Naruya Saitou,Elena Ciani,Pamela A. Burger +9 more
TL;DR: Using a genome-wide approach, the authors are able to infer patterns of migration following domestication, which follow known historic caravan routes, and identify major population expansions and bottlenecks through history.
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Hitchhiking the high seas: Global genomics of rafting crabs
TL;DR: The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to the understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms.
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