Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple

2021 ◽  
Author(s):  
Yongpeng Ma ◽  
Detuan Liu ◽  
Hafiz Muhammad Wariss ◽  
Rengang Zhang ◽  
Lidan Tao ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Analysis ◽  
Population Genomic

scholarly journals The Drosophila Genome Nexus: a population genomic resource of 605 Drosophila melanogaster genomes, including 197 genomes from a single ancestral range population

2014 ◽  
Author(s):  
Justin Lack ◽  
Charis Cardeno ◽  
Marc Crepeau ◽  
William Taylor ◽  
Russ Corbett-Detig ◽  
...  
Keyword(s):  
Population Genomics ◽  
Demographic History ◽  
Genetic Research ◽  
Genomic Analysis ◽  
Data Sets ◽  
Large Sample Size ◽  
Drosophila Genome ◽  
High Genetic Diversity ◽  
Population Genomic ◽  
Variant Detection

Hundreds of wild-derived D. melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach, and settled on an assembly strategy that utilizes two alignment programs and incorporates both SNPs and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets (previous DPGP releases and the DGRP freeze 2.0), and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 605 consistently aligned genomes, and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets.

scholarly journals Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii)

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e77175 ◽  
Author(s):  
Xin Ma ◽  
Joanna L. Kelley ◽  
Kirsten Eilertson ◽  
Shaila Musharoff ◽  
Jeremiah D. Degenhardt ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Analysis ◽  
Pongo Pygmaeus ◽  
Pongo Abelii ◽  
Population Genomic ◽  
History Of

scholarly journals Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

2009 ◽  
Vol 26 (6) ◽  
pp. 1357-1367 ◽  
Author(s):  
Laura B. Scheinfeldt ◽  
Shameek Biswas ◽  
Jennifer Madeoy ◽  
Caitlin F. Connelly ◽  
Eric E. Schadt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Population Genomic ◽  
Complex Evolutionary History

Population genomic analysis reveals domestication of cultivated rye from weedy rye

2021 ◽  
Author(s):  
Yanqing Sun ◽  
Enhui Shen ◽  
Yiyu Hu ◽  
Dongya Wu ◽  
Yu Feng ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Population Genomic

Comparative population genomic analysis provides insights into breeding of modern indica rice in China

Gene ◽  
2021 ◽  
Vol 768 ◽  
pp. 145303
Author(s):  
Chao Qin ◽  
Yanru Guo ◽  
Jianzhuang Wu ◽  
Long Wang ◽  
Milton Brian Traw ◽  
...  
Keyword(s):  
Indica Rice ◽  
Genomic Analysis ◽  
Population Genomic ◽  
Comparative Population

scholarly journals Understanding pneumococcal serotype 1 biology through population genomic analysis

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Chrispin Chaguza ◽  
◽  
Jennifer E. Cornick ◽  
Simon R. Harris ◽  
Cheryl P. Andam ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Population Genomic ◽  
Serotype 1 ◽  
Pneumococcal Serotype
Sign in / Sign up

Export Citation Format

Share Document