scholarly journals PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

2014 ◽  
Vol 31 (7) ◽  
pp. 1929-1936 ◽  
Author(s):  
Bastian Pfeifer ◽  
Ulrich Wittelsbürger ◽  
Sebastian E. Ramos-Onsins ◽  
Martin J. Lercher
Keyword(s):  
Population Genomic ◽  
Genomic Analyses

scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

scholarly journals Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

2019 ◽  
Vol 51 (7) ◽  
pp. 1187-1189
Author(s):  
Jarkko Salojärvi ◽  
Olli-Pekka Smolander ◽  
Kaisa Nieminen ◽  
Sitaram Rajaraman ◽  
Omid Safronov ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Silver Birch ◽  
Adaptive Landscape ◽  
Population Genomic ◽  
Genomic Analyses

scholarly journals Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River

2020 ◽  
Vol 8 (6) ◽  
pp. 471
Author(s):  
Nguyen Thanh Vu ◽  
Tran Thi Thuy Ha ◽  
Vo Thi Bich Thuy ◽  
Vu Thi Trang ◽  
Nguyen Hong Nguyen
Keyword(s):  
Genetic Diversity ◽  
Mekong River ◽  
Effective Population ◽  
Wild Stock ◽  
Pangasianodon Hypophthalmus ◽  
Population Genomic ◽  
Diversity Assessment ◽  
Genomic Analyses ◽  
In The Wild ◽  
Striped Catfish

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

scholarly journals Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

2017 ◽  
Vol 26 (4) ◽  
pp. 1131-1147 ◽  
Author(s):  
Brittany S. Barker ◽  
Krikor Andonian ◽  
Sarah M. Swope ◽  
Douglas G. Luster ◽  
Katrina M. Dlugosch
Keyword(s):  
Range Expansion ◽  
Centaurea Solstitialis ◽  
Yellow Starthistle ◽  
Trait Evolution ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of

scholarly journals Linked-read sequencing enables haplotype-resolved resequencing at population scale

2020 ◽  
Author(s):  
Dave Lutgen ◽  
Raphael Ritter ◽  
Remi-André Olsen ◽  
Holger Schielzeth ◽  
Joel Gruselius ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Genome Resequencing ◽  
High Coverage ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of ◽  
Population Scale ◽  
Haplotype Information

AbstractThe feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and the inference of selective sweeps – are still limited by the lack of high-quality haplotype information. In this respect, the newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of the phased sequence located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90), respectively. Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Finally, phasing contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing data at population scale.

scholarly journals Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

2013 ◽  
Vol 77 (3) ◽  
pp. 430-442 ◽  
Author(s):  
Pei Xu ◽  
Shizhong Xu ◽  
Xiaohua Wu ◽  
Ye Tao ◽  
Baogen Wang ◽  
...  
Keyword(s):  
Bottle Gourd ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Low Coverage

Comparative population genomic analyses of the reconstructed local breed “Nero di Parma” with other commercial and autochthonous Italian pig breeds

2020 ◽  
Vol 235 ◽  
pp. 104014
Author(s):  
Giuseppina Schiavo ◽  
Samuele Bovo ◽  
Silvia Tinarelli ◽  
Hamed Kazemi ◽  
Maurizio Gallo ◽  
...  
Keyword(s):  
Local Breed ◽  
Pig Breeds ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Comparative Population

scholarly journals The genomics of ecological vicariance in threespine stickleback fish

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Marius Roesti ◽  
Benjamin Kueng ◽  
Dario Moser ◽  
Daniel Berner
Keyword(s):  
Molecular Level ◽  
Parallel Evolution ◽  
Threespine Stickleback ◽  
Ancestral Population ◽  
Selective Sweeps ◽  
Population Genomic ◽  
Genomic Analyses ◽  
The Face ◽  
Freshwater Stickleback ◽  
Different Populations

Abstract Populations occurring in similar habitats and displaying similar phenotypes are increasingly used to explore parallel evolution at the molecular level. This generally ignores the possibility that parallel evolution can be mimicked by the fragmentation of an ancestral population followed by genetic exchange with ecologically different populations. Here we demonstrate such an ecological vicariance scenario in multiple stream populations of threespine stickleback fish divergent from a single adjacent lake population. On the basis of demographic and population genomic analyses, we infer the initial spread of a stream-adapted ancestor followed by the emergence of a lake-adapted population, that selective sweeps have occurred mainly in the lake population, that adaptive lake–stream divergence is maintained in the face of gene flow from the lake into the streams, and that this divergence involves major inversion polymorphisms also important to marine-freshwater stickleback divergence. Overall, our study highlights the need for a robust understanding of the demographic and selective history in evolutionary investigations.

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