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Poster Full Abstracts - Evolution and Quantitative Genetics
Poster board number is above title. The first author is the presenter
269
513C
Polymorphisms in chromatin accessibility state within
D.melanogaster
.
Aaron Hardin
1
, Xiao-Yong Li
2
, Michael Eisen
1,2,3
. 1) Molecular and Cell
Biology, University of California, Berkeley, Berkeley, CA; 2) California Institute of Quantitative Biology, University of California, Berkeley, Berkeley, CA;
3) Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA.
The early embryo of
D. melanogaster
has several of the best studied gene regulatory networks in animals. In particular, the factors that regulate anterior-
posterior patterning were identified by genetic methods several decades ago, and we now well understand many of their activities, expression patterns and
targets. Previous work in the Eisen lab has shown that these factors bind to thousands of regions across the genome. Our lab has measured transcription
factor binding in both
D. melanogaster
and the relatively closely related species
D. yakuba
but have been unable to predict the underlying sequence changes
that influence these changes due to the large number of polymorphisms between species. However, correlated changes in binding across factors suggests that
the underlying chromatin state may be playing a significant role in binding divergence. We have now examined chromatin state in several natural isolates of
D. melanogaster
by measuring genome wide DNase-hypersensitivity with high-throughput sequencing during the early embryo. The regions of
hypersensitivity strongly correlate with nucleosome free regions and regions of bound transcription factors. In order to identify the sequence polymorphisms
and correlate these with changes in chromatin state, we have pooled DNAse treated chromatin from several natural isolates and compared the frequency of
recovered regions to the frequency of the polymorphisms present in our sample.
514A
Unpacking Estimates of Cis-regulatory Variation.
Bradley J. Main
1
, Andrew Smith
1
, Rita Graze
2
, Marta Wayne
2
, Lauren McIntyre
2
, Sergey Nuzhdin
1
. 1)
MCB, Univ Southern California, Los Angeles, CA; 2) Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611.
The accumulation of regulatory variants in cis (at the gene) contributes to diversity between populations and divergence between species of Drosophila. In
this study, we uncover potential non-additive cis-by-trans interactions within Drosophila simulans, which may be confounded in preliminary estimates of cis.
Furthermore, we demonstrate that transcription start sites (TSSs) are not fixed genetic features between species, but rather, are likely an important
component of functional cis-regulatory variation. We employ a custom, allele-specific microarray to survey allelic imbalance transcriptome-wide in a sample
population of D. simulans. Cis-regulatory variation was exclusively estimated from allele-specific expression (ASE) assays in F1 hybrids, where the trans
and environmental factors are shared equally between alleles. Then, we compared ASE between F1 hybrids and introgression F1 hybrids. The introgression
F1's are identical to the full F1 hybrids, except they are homozygous for the tester line outside of the 12Mb introgression region on chromosome three. Thus,
a change in ASE between these genotypes would only be explained by cis-by-trans interactions. To investigate changes in TSSs, we developed a new
technique to target TSSs and applied this to four species within the D. melanogaster subgroup (D.melanogaster, D. simulans, D. sechellia, and D. mauritiana)
and D. pseudoosbcura. This data in combination with publically available genome alignments between species was used to make inferences about the extent
of TSS differences over evolutionary time. From these results, we show that TSS divergence increases with predicted phylogenetic distance, suggesting that
changes in these cis-regulatory features are common and may contribute to species differences. Furthermore, among genes with divergent TSSs, we test for
enrichment of low or highly expressed genes, association with gene duplication events, and enrichment of specific gene ontology categories.
515B
Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture.
John E. Pool
1
, Kristian A. Stevens
2
,
Marc Crepeau
2
, Charis M. Cardeno
2
, James J. Emerson
3
, Russell Corbett-Detig
4
, Pablo Duchen
5
, David J. Begun
2
, Charles H. Langley
2
. 1) Laboratory of
Genetics, University of Wisconsin - Madison, Madison, WI; 2) Department of Evolution and Ecology, University of California - Davis, Davis, CA; 3)
Department of Integrative Biology, University of California - Berkeley, Berkeley, CA; 4) Department of Organismal and Evolutionary Biology, Harvard
University, Cambridge, MA; 5) Section of Evolutionary Biology, Ludwig Maximilians Universitat Munchen, Munich, Germany.
Populations from the African ancestral range of
Drosophila melanogaster
are the species’ richest source of genetic variation, and may hold the keys to
understanding the adaptation and demography in worldwide populations. We describe the preliminary analysis of >100 fully sequenced genomes from
African populations of
D. melanogaster
.Sequencing utilized an Illumina Genome Analyzer IIx, in most cases using 76bp paired end reads with ~300bp
inserts, with an average sequencing depth of 30X. Genomes were fully homozygous because genomic DNA was amplified from haploid embryos. These
genomes originate from >20 sub-Saharan locations. Using a novel Hidden Markov Model admixture detection algorithm, we inferred high levels of
cosmopolitan (non-sub Saharan) admixture in populations from across the African continent. Admixture proportions varied dramatically among samples,
even within small geographic regions. Based on the megabase scale of admixture intervals, large-scale introgression appears to be a very recent
phenomenon. Admixture proportions also differed starkly within samples, potentially indicating isolation mechanisms within populations. Populations from
south of the Congo Basin were then found to have the highest levels of nucleotide diversity, and may represent the ancestral range of the species. Moderate
levels of genetic structure were found across the African continent, and populations from central Africa were found to have the closest relationships with
cosmopolitan populations. Evidence of adaptive differences between African populations was also apparent.
516C
Patterns of natural variation unravel strong ongoing genomic conflict in
Drosophila mauritiana
.
Christian W. Schloetterer, Viola Nolte, Ram Vinay
Pandey, Robert Kofler. Inst f Populationsgenetik, Vetmeduni Vienna, Wien.
Drosophila mauritiana
, a close relative of
D. melanogaster
, is endemic to a few islands in the Indian ocean. Despite that
D. mauritiana
serves as an
important model to understand the genetic basis of speciation processes, its genome sequence is not yet available, and natural variation has been
characterized only for a few loci. We generated a draft genome of
D. mauritiana
and characterized the genome-wide polymorphisms by sequencing pooled
individuals (Pool-Seq). We resolve the long-debated phylogenetic relationship within the
D. simulans
clade by showing that
D. mauritiana
and
D. simulans
are more closely related while
D. sechellia
is the most diverged species. Consistent with large amounts of shared polymorphism, we find no evidence for a
faster X chromosome evolution within the
D. simulans
group, but a very pronounced effect in comparisons involving either
D. melanogaster
or
D. yakuba
.
We demonstrate how the well-documented change in recombination landscape in
D. mauritiana
affects the portioning of variation along the chromosomes:
regions close to the centromere which exhibit low variation and reduced selection efficacy in
D. melanogaster
show normal polymorphism levels and no
enrichment of non-synonymous changes in
D. mauritiana
. Finally, we report the genomic signatures of ongoing genomic conflict in
D. mauritiana
. Two