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An analysis of genetic changes during the divergence of Drosophila species.

Sousa-Neves R, Rosas A - PLoS ONE (2010)

Bottom Line: We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster.Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America. rui.sousaneves@case.edu

ABSTRACT

Background: It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species.

Principal findings: In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.

Conclusions: Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

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Distribution of ancestral alleles in the three major chromosomes.The 20 division coordinates used are those of D. melanogaster. Almost all divisions have one or more ancestral alleles. The dashed lines indicate the average number of alleles plus one standard deviation. Note that some divisions have a higher density of ancestral alleles than others.
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pone-0010485-g003: Distribution of ancestral alleles in the three major chromosomes.The 20 division coordinates used are those of D. melanogaster. Almost all divisions have one or more ancestral alleles. The dashed lines indicate the average number of alleles plus one standard deviation. Note that some divisions have a higher density of ancestral alleles than others.

Mentions: We next tested whether the ancestral alleles are clustered in specific genomic locations or whether they appear evenly distributed across the genome. To address this issue we plotted their occurrence along the 20 divisions of the major chromosomes, using chromosomal coordinates of D. melanogaster [20] (Fig. 3). Since the method of averages and standard deviations produces a distortion that results in fewer common genes on the X chromosome, we used the results obtained from the percentile search to plot the position of these genes. Our data suggest that although these alleles can be found in almost every division of the three major chromosomes, some regions are hotspots for ancestral alleles. These regions were identified by searching for regions that have more ancestral alleles than the average plus 1 standard deviation. In particular, the X chromosome division 1 and division 9 have more ancestral alleles than most divisions on this chromosome. Similarly, three divisions on the left arm of the second chromosome (i.e. 22, 23 and 34) also harbor more ancestral alleles than the average plus one standard deviation for this arm. The right arm of the second chromosome also seems to have three hotspots in divisions 44, 54 and 59, while the distribution of ancestral alleles on the left arm of the third chromosome does not contain prominent hotspots, except perhaps by divisions 61, 64, 68 and 70. Finally, on the right arm of the third chromosome, one prominent hotspot appears at division 82. The significance of this clustering is not yet clear, but we note that some of these hotspots are located nearby known rearrangement breakpoints observed in D. simulans such as in divisions 1–2, divisions 21–22, 59–60 and 82 [21].


An analysis of genetic changes during the divergence of Drosophila species.

Sousa-Neves R, Rosas A - PLoS ONE (2010)

Distribution of ancestral alleles in the three major chromosomes.The 20 division coordinates used are those of D. melanogaster. Almost all divisions have one or more ancestral alleles. The dashed lines indicate the average number of alleles plus one standard deviation. Note that some divisions have a higher density of ancestral alleles than others.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2864749&req=5

pone-0010485-g003: Distribution of ancestral alleles in the three major chromosomes.The 20 division coordinates used are those of D. melanogaster. Almost all divisions have one or more ancestral alleles. The dashed lines indicate the average number of alleles plus one standard deviation. Note that some divisions have a higher density of ancestral alleles than others.
Mentions: We next tested whether the ancestral alleles are clustered in specific genomic locations or whether they appear evenly distributed across the genome. To address this issue we plotted their occurrence along the 20 divisions of the major chromosomes, using chromosomal coordinates of D. melanogaster [20] (Fig. 3). Since the method of averages and standard deviations produces a distortion that results in fewer common genes on the X chromosome, we used the results obtained from the percentile search to plot the position of these genes. Our data suggest that although these alleles can be found in almost every division of the three major chromosomes, some regions are hotspots for ancestral alleles. These regions were identified by searching for regions that have more ancestral alleles than the average plus 1 standard deviation. In particular, the X chromosome division 1 and division 9 have more ancestral alleles than most divisions on this chromosome. Similarly, three divisions on the left arm of the second chromosome (i.e. 22, 23 and 34) also harbor more ancestral alleles than the average plus one standard deviation for this arm. The right arm of the second chromosome also seems to have three hotspots in divisions 44, 54 and 59, while the distribution of ancestral alleles on the left arm of the third chromosome does not contain prominent hotspots, except perhaps by divisions 61, 64, 68 and 70. Finally, on the right arm of the third chromosome, one prominent hotspot appears at division 82. The significance of this clustering is not yet clear, but we note that some of these hotspots are located nearby known rearrangement breakpoints observed in D. simulans such as in divisions 1–2, divisions 21–22, 59–60 and 82 [21].

Bottom Line: We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster.Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America. rui.sousaneves@case.edu

ABSTRACT

Background: It has been long appreciated that speciation involves changes in body plans and establishes genetic, reproductive, developmental and behavioral incompatibilities between populations. However, little is still known about the genetic components involved in these changes or the sequence and scale of events that lead to the differentiation of species.

Principal findings: In this paper, we investigated the genetic changes in three closely related species of Drosophila by making pair-wise comparisons of their genomes. We focused our analysis on the modern relatives of the alleles likely to be segregating in pre-historic populations at the time or after the ancestor of D. simulans became separated from the ancestor of D. melanogaster. Some of these genes were previously implicated in the genetics of reproduction and behavior while the biological functions of others are not yet clear.

Conclusions: Together these results identify different classes of genes that might have participated in the beginning of segregation of these species millions of years ago in Africa.

Show MeSH