In this paper, Molly
K. Burke and his collogues did an experimental evolution systems, which allows
the genomic study of adaptation. They selected outbred, sexually reproducing, replicated
populations of Drosophila melanogaster, which experienced over 600
generations of laboratory selection for accelerated development.
Short-read sequences
from three genomic DNA libraries, were obtained using Illumina platform, they
are as follows:
a)
A pooled sample of
five replicate populations that have undergone sustained selection for
accelerated development and early fertility for over 600 generations (ACO);
b)
A pooled sample of
five replicate ancestral control populations, which experience no direct
selection on development time (CO);
c)
A single ACO
replicate population (ACO1);
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| Figure 1: Phenotypic divergence in the selection treatments |
In the above figure,
the grey bar indicates values measured in the ACO and CO treatments for each of
the five replicate populations. B indicates replicate populations, which
represent phenotypes typical of populations kept on two-week generation
maintenance schedules.
This figure shows a
comparative analysis between the ACO population and the population with the CO
treatment. Every time, ACO featured significantly differentiated phenotypes,
including shorter development time and reductions in pre-adult viability,
longevity, adult body size and stress resistance. Furthermore, the CO treatment
does not show stringent selection, as it entails no more than moderate
selection for postponed reproduction, resulting in moderately increased development
time and longevity.
 |
| Figure 2: Differentiation throughout the genome |
A 100-kb genome-wide
sliding-window analysis test was carried out to identify regions diverged in
allele frequency between the ACO and CO libraries and between the ACO and ACO1
libraries. This is due to the fact that, linkage disequilibrium in individual
ACO and CO replicate populations may extend anywhere from 20 to 100 (kb). The
five different panels are basically for the five major D. melanogaster
chromosome arms.
It identifies a
large number of genomic regions showing significant divergence between the
accelerated development populations and their matched controls depicted by
black lines in Figure 2, and very little divergence is observed between a
single replicate evolved population (ACO1) and the pooled sample consisting of
all five ACO populations and this is indicated by the grey lines. The dotted
line is the threshold that any given window has a 0.1% chance of exceeding
relative to the genome-wide level of noise. Interestingly, an excess of
diverged regions on the X chromosome relative to on the autosomes is very
evident. This observation is only expected if adaptation were driven by
selection on initially rare recessive or partially recessive alleles. Furthermore,
the sharpness of the peaks suggests that regions of the genome that have responded
to experimental evolution are precisely identified. However, even the sharpest
peaks tend to delineate, 50–100-kb regions.
Kaplan et al. stated
that, recent research on evolutionary genetics has focused on classic selective
sweeps. In a recombining
region, a selected sweep is expected to reduce heterozygosity at SNPs flanking
the selected site.
 |
|
Figure 3:
Heterozygosity throughout the genome
|
Figure 3, shows a similar
sliding-window analysis (100 kb) of heterozygosity in ACO and CO lines
suggesting that there are indeed local losses of heterozygosity, which is
depicted by the red and the blue lines, respectively. Heterozygosity in ACO1
depicted by grey line, shows remarkable concordance with the reductions in
heterozygosity in the ACO pool. Regions of reduced heterozygosity are strongly
associated with regions of differentiated allele frequency. Interestingly, we
observed no location in the genome where heterozygosity is reduced to anywhere
near zero, and therefore, it lacks the evidence for a classic sweep is a
feature of the data regardless of window size. Nevertheless, both the figure 2
and 3 are quite similar.
 |
|
Figure 4: Analysis
of individual genotypes, measured by cleaved amplified
polymorphic sequence
(CAPS) techniques.
|
Figure 4a shows the allele
frequency estimates of the most common allele at 30 SNPs genotyped in 35
females per replicate population. Red circles and grey squares represent ACO
and CO estimates. Open symbols are allele frequencies for ACO1–ACO5 and
CO1–CO5, and filled symbols represent treatment means. Alternating black and
grey bars designate the X, 2L, 2R, 3L, and 3R arms, respectively. The grey
lines indicate SNP location. We observe that replicate populations within a
selection treatment have very similar allele frequencies.
In Figure 4b, we see
a scatter plot comparing allele frequency estimates at the same 30 SNPs
obtained from the Illumina resequencing versus individual genotyping. Red circles
represent ACO, black squares represent CO and the straight line represents a
slope of unity. Here we see that individual genotypes are consistent with
allele frequency estimates from the resequenced pooled libraries.
Therefore, it can be
concluded that the congruence in allele frequencies and patterns of
heterozygosity between the ACO1 and ACO libraries is unlikely to be some sort
of artefact of sample preparation or data analysis.
The study shows a convergence
of allele frequencies and heterozygosity levels between replicate populations.
This convergence might be due to selection, acting on the same
intermediate-frequency variants in each population. Under this scenario,
convergence in allele frequencies is due to parallel evolution. Another reason
could be, unwanted migration between replicate populations, even at very low
levels.
Conclusively, it was very interesting to see that despite strong selection, Molly K. Burke and
his collogues failure to observe the signature of a classic sweep in these populations.
This didn't make it simpler to understand
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