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Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura.

Simões P, Pascual M, Santos J, Rose MR, Matos M - BMC Evol. Biol. (2008)

Bottom Line: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied.Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process.We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Departamento de Biologia Animal, Campo Grande, 1749-016 Lisboa, Portuga. pmsimoes@fc.ul.pt

ABSTRACT

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources.

Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus.

Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

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Standardized Heterozygosity ratios (Ln RH) between generations 14 and 40. Ln RH ratios (H40/H14) for AR (Fig. 2A) and TW (Fig. 2B) populations. Dashed lines represent the 95% confidence interval of the standardized normal distribution. Positive Ln RH values correspond to increases in variation through time.
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Figure 2: Standardized Heterozygosity ratios (Ln RH) between generations 14 and 40. Ln RH ratios (H40/H14) for AR (Fig. 2A) and TW (Fig. 2B) populations. Dashed lines represent the 95% confidence interval of the standardized normal distribution. Positive Ln RH values correspond to increases in variation through time.

Mentions: Between generations 14 and 40, Ln RH ratios for the AR populations were similar to those mentioned above, again with only locus dsub14 significantly differing from all other loci (post hoc Scheffé test; p < 0.05 for all comparisons). This was also observed for each replicate population by analyzing the standardized Ln RH values (see Fig. 2). During this second period of laboratory evolution, the frequencies of the potentially selected allele in locus dsub14 continued to rise in AR1 and AR2 populations (with the 116 bp allele reaching a frequency of 27.8 and 41.4% at generation 40, respectively). Nevertheless, in the AR3 population the allele that had previously increased in frequency (120 bp) slightly decreased (from 19.2% to 13.5%), being the high Ln RH ratio due to the increase in frequency of other alleles. For the TW populations, no significant differences between loci were detected with the general ANOVA or the Scheffé test. However, the analysis of the standardized Ln RH values for each TW replicate population showed some significant results, though they were not consistent among replicates. Specifically, locus dsub14 showed a significant decrease in heterozygosity in the TW2 population, due to a decrease in frequency of the 120 bp allele. Heterozygosities for this particular locus remained almost constant in the TW1 and TW3 populations during this period (see Fig. 2).


Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura.

Simões P, Pascual M, Santos J, Rose MR, Matos M - BMC Evol. Biol. (2008)

Standardized Heterozygosity ratios (Ln RH) between generations 14 and 40. Ln RH ratios (H40/H14) for AR (Fig. 2A) and TW (Fig. 2B) populations. Dashed lines represent the 95% confidence interval of the standardized normal distribution. Positive Ln RH values correspond to increases in variation through time.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2266711&req=5

Figure 2: Standardized Heterozygosity ratios (Ln RH) between generations 14 and 40. Ln RH ratios (H40/H14) for AR (Fig. 2A) and TW (Fig. 2B) populations. Dashed lines represent the 95% confidence interval of the standardized normal distribution. Positive Ln RH values correspond to increases in variation through time.
Mentions: Between generations 14 and 40, Ln RH ratios for the AR populations were similar to those mentioned above, again with only locus dsub14 significantly differing from all other loci (post hoc Scheffé test; p < 0.05 for all comparisons). This was also observed for each replicate population by analyzing the standardized Ln RH values (see Fig. 2). During this second period of laboratory evolution, the frequencies of the potentially selected allele in locus dsub14 continued to rise in AR1 and AR2 populations (with the 116 bp allele reaching a frequency of 27.8 and 41.4% at generation 40, respectively). Nevertheless, in the AR3 population the allele that had previously increased in frequency (120 bp) slightly decreased (from 19.2% to 13.5%), being the high Ln RH ratio due to the increase in frequency of other alleles. For the TW populations, no significant differences between loci were detected with the general ANOVA or the Scheffé test. However, the analysis of the standardized Ln RH values for each TW replicate population showed some significant results, though they were not consistent among replicates. Specifically, locus dsub14 showed a significant decrease in heterozygosity in the TW2 population, due to a decrease in frequency of the 120 bp allele. Heterozygosities for this particular locus remained almost constant in the TW1 and TW3 populations during this period (see Fig. 2).

Bottom Line: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied.Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process.We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Universidade de Lisboa, Faculdade de Ciências da Universidade de Lisboa, Centro de Biologia Ambiental, Departamento de Biologia Animal, Campo Grande, 1749-016 Lisboa, Portuga. pmsimoes@fc.ul.pt

ABSTRACT

Background: Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources.

Results: We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus.

Conclusion: Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution.

Show MeSH