Supplementary data for: Genetic Diversity of Bactrocera dorsalis (Diptera: Tephritidae) on the Hawaiian Islands: Implications for an Introduction Pathway Into California

2014 ◽  
Keyword(s):  
Genetic Diversity ◽  
Hawaiian Islands ◽  
Bactrocera Dorsalis ◽  
Supplementary Data ◽  
Introduction Pathway

scholarly journals Genetic Diversity of Bactrocera dorsalis (Diptera: Tephritidae) on the Hawaiian Islands: Implications for an Introduction Pathway Into California

2014 ◽  
Vol 107 (5) ◽  
pp. 1946-1958 ◽  
Author(s):  
Norman B. Barr ◽  
Lisa A. Ledezma ◽  
Luc Leblanc ◽  
Michael San Jose ◽  
Daniel Rubinoff ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hawaiian Islands ◽  
Bactrocera Dorsalis ◽  
Introduction Pathway

scholarly journals ATLAS: Analysis Tools for Low-depth and Ancient Samples

2017 ◽  
Author(s):  
Vivian Link ◽  
Athanasios Kousathanas ◽  
Krishna Veeramah ◽  
Christian Sell ◽  
Amelie Scheu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ancient Dna ◽  
State Of The Art ◽  
Supplementary Information ◽  
Post Mortem ◽  
Supplementary Data ◽  
Supplementary Material ◽  
C Program ◽  
User Friendly ◽  
Proper Analysis

AbstractSummaryPost-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamage 2.0.AvailabilityATLAS is an open-source C++ program freely available at https://bitbucket.org/phaentu/[email protected] informationSupplementary data are available at Bioinformatics online.

Supplementary data: Assessment of genetic diversity ofLycoris longituba (Amaryllidaceae) detected by RAPDs

2006 ◽  
Vol 85 (3) ◽  
pp. 205-205 ◽  
Author(s):  
Chuan-Liang Deng ◽  
Jian Zhou ◽  
Wu-Jun Gao ◽  
Fu-Cong Sun ◽  
Rui-Yun Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Supplementary Data ◽  
Data Assessment

scholarly journals Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

2021 ◽  
Author(s):  
Timothy A. Crombie ◽  
Paul Battlay ◽  
Robyn E. Tanny ◽  
Kathryn S. Evans ◽  
Claire M. Buchanan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Caenorhabditis Elegans ◽  
Local Adaptation ◽  
Balancing Selection ◽  
Sampling Site ◽  
Hawaiian Islands ◽  
Pathogen Resistance ◽  
Pacific Rim ◽  
High Genetic Diversity ◽  
C Elegans

AbstractThe nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Wild C. elegans have been isolated from both temperate and tropical climates, where they feed on bacteria associated with decomposing plant material. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. The high genetic diversity found there suggests that: (1) the origin of the species lies in Hawaii or the surrounding Pacific Rim; and (2) the ancestral niche of the species is likely similar to the Hawaiian niche. A recent study of the Hawaiian niche found that genetically distinct groups appeared to correlate with elevation and temperature, but the study had a limited sample size. To better characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three-year period, measured various environmental parameters at each sampling site, and whole-genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche is moderately moist native forests at high elevations (500 to 1500 meters) where temperatures are cool (15 to 20°C). We measured levels of genetic diversity and differentiation among Hawaiian strains and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyperdivergent regions, which are likely maintained by balancing selection and enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and a possible genetic basis for this adaptation.

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