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Article
Open AccessHapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent hi...
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Article
Open AccessGenomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses
The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representative...
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Article
Open AccessThe gene structure and hypervariability of the complete Penaeus monodon Dscam gene
Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a t...
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Article
Open AccessStructural variants exhibit widespread allelic heterogeneity and shape variation in complex traits
It has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs fro...
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Article
Open AccessGenome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster
Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any ...
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Article
Genome-wide analysis of a long-term evolution experiment with Drosophila
Until now, experimental evolution has been largely performed in asexual systems with small genomes, such as bacteria and yeast. Burke et al. report results of a genome-wide study in Drosophila melanogaster fruitf...
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Evolutionary Nutrigenomics
In contrast to the common view that aging is due to accumulated damage or disorder, we have demonstrated that natural selection can readily extend lifespan by selecting many small-effect changes in gene expres...
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Article
Experimental evolution reveals natural selection on standing genetic variation
Henrique Teotónio and colleagues report a comprehensive study of the molecular population genetics of adaptation and reverse evolution in Drosophila. They conclude that adaptive reverse evolution in this context ...
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Article
Open AccessFine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, re...
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Article
Open AccessA wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model
Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value...
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Article
Open AccessA low-cost open-source SNP genoty** platform for association map** applications
Association map** aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genoty** a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of in...
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Article
Contribution of Distal-less to quantitative variation in butterfly eyespots
The colour patterns decorating butterfly wings provide ideal material to study the reciprocal interactions between evolution and development. They are visually compelling products of selection, often with a cl...
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Article
A correction for allele frequency estimates derived from isofemale lines
Isofemale lines are commonly used inDrosophila and other genera for the purpose of assaying genetic variation. Isofemale lines can be kept in the laboratory for many generations before genetic work is carried out...
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Article
A correction for allele frequency estimates derived from isofemale lines
Isofemale lines are commonly used inDrosophila and other genera for the purpose of assaying genetic variation. Isofemale lines can be kept in the laboratory for many generations before genetic work is carried out...
