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Full Abstracts – EVOLUTION AND QUANTITATIVE GENETICS I
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105
The impact of mutational biases and positive selection on the distribution of Copy Number Variants among five worldwide populations of
Drosophila melanogaster
.
Margarida Cardoso-Moreira, Jennifer K. Grenier, Andrew G. Clark. Molecular Biology and Genetics, Cornell University, Ithaca,
NY.
Copy Number Variants (i.e. duplications, deletions and insertions of DNA segments) can create novel genes, alter gene structures, modify gene regulation
and dosage, and abolish gene function. They are widespread in genomes and underlie a wide range of phenotypes ranging from lethal to adaptive. In order to
understand the impact of mutation and selection in shaping patterns of CNVs, we set out to identify CNVs in the genomes of 92
D. melanogaster
lines
originating from five geographical locations (United States, Netherlands, Australia, China and Zimbabwe). The genomes of these 92 lines were fully
sequenced using Illumina paired-end technology and CNVs larger than 25 bp were identified using a bioinformatics pipeline that combined read-pair and
split-read methods to identify the exact breakpoints of the CNVs, an essential requirement to understand the functional impact of these variants. We
identified ~150,000 variants, mostly small insertions/duplications and deletions, but also complete gene duplications and deletions, retroposed genes and
novel gene structures. We carried out extensive validation of these variants by PCR and Sanger sequencing. The distribution of CNVs throughout the
genomes, between individuals and between populations, was strongly shaped by both mutational biases and natural selection. Regarding mutation, we found
the distribution of duplications and deletions to be highly non-random, with duplication and deletion hotspots identified throughout the genome. We
investigated the causes underlying the existence of hotspots by associating their presence with: 1) DNA replication timing; 2) chromatin accessibility; and 3)
presence of non-B DNA structures. Regarding selection, we found purifying selection to be pervasive, eliminating most variants associated with functional
regions. However, by leveraging haplotype information with levels of population differentiation we also found evidence for positive selection acting on a
subset of the CNVs.
106
Variation in Genome Structure in
Drosophila yakuba
.
Rebekah L. Rogers, Kevin R. Thornton. Ecology and Evolutionary Biology, Thornton Lab, Irvine,
CA.
Chromosomal rearrangements, which shuffle the locations of genes within the genome, can cause changes in where and when neighboring genes are
expressed. If these rearrangements do not respect gene boundaries, they may also split genes into pieces and combine them with other genetic material,
thereby modifying the proteins that the genome produces. We have used paired-end Illumina sequencing reads to identify chromosomal rearrangements in
20 inbred strains recently derived from natural populations of
D. yakuba
. Chromosomal rearrangements can be identified through paired end reads that map
in parallel rather than properly paired orientation or which map to distant sections of the genome. Using these criteria we have identified over 200 putative
chromosomal rearrangements segregating within the population. Some 15% of these events contain breakpoints that fall within genes, suggesting that the
species houses a vast amount of diversity in gene content as well as exceptional variation in genome structure.
107
Evolution of New Genes with Essential Functions in Drosophila Development and Reproduction.
Sidi Chen, Manyuan Long. Dept Ecology &
Evolution, The University of Chicago, Chicago, IL 60637.
Essential genes are often portrayed as conserved and ancient, while younger lineage-specific genes have been considered to be more dispensable and to
perform relatively minor organismal functions. It is unclear how essential genes arise and how new genes accumulate essential functions. To investigate the
origin and evolution of essential genes, we used newly evolved genes as a model. Because new genes arise continuously through time, and, when first arose,
they were expected to be non-essential since their immediate ancestral species survived without them, thus they must subsequently evolve essentiality.
However, little is known about the phenotypes and degrees of essentiality for new genes. We identified over five hundred new gene origination events in the
last 35 million years. We phenotyped 195 newly arisen genes with RNAi knocking down and found that 30% of lethal. Interestingly, the proportion of lethal
genes is similar in every evolutionary age group that we examined. Lethality was highly enriched in the pupal stage, and also found in the larval stages.
Lethality was attributed to diverse cellular and developmental defects, such as organ formation and patterning defects. Our data suggested that new genes
frequently and rapidly evolve essential functions. In addition, we assayed adult stage phenotypes of the genes that are not essential for pre-adult stage
development. We found a large proportion of them played essential roles in reproduction in both males and females. The mechanism for the evolution of
essentiality would change with the types of new genes. A de novo gene has to evolve essentiality through neofunctionalization. A duplicated gene, generated
from a parental copy, could become essential from the lost of parents, the switch of essentiality from paralogs, subfunctionalization, or neofunctionalization.
Evolutionary analyses revealed strong Darwinian selection and structure renovation for these genes, as well as their independent essentiality from parental
genes, support the neofunctionalization origin as a primary mechanism.