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Background  The current analysis of transposon elements (TE) in  Drosophila melanogaster  at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies ( D. melanogaster ) from the ecologically tropic, hot, and dry south-facing slope (SFS) or “African” slope (AS) of EC and compared it with the TE frequencies on the temperate-cool and humid north-facing slope (NFS) or “European” slope (ES), separated, on average, by 250 m. The flies were sampled from two stations on each slope. We received their results, including the frequencies of each TE on each slope, and the probabilities of the statistical analyses (G-tests) of each TE separately. We continued the analysis of the inter-slope differences of the frequencies of the TEs, and based our different conclusions on that analysis and on the difference between micro (=EC) and macro (2000 km.) comparisons [Gonzalez et al. 2015 doi:10.1186/s13062-015-0075-4].    Results  Our collaborators based all their conclusions on the non-significant results of each of the individual tests of the 28 TEs. We analysed also the distribution of the TE differences between the slopes, based on their results. Thirteen TEs were more frequent on the SFS, 11 were more frequent on the NFS, and four had equal frequencies. Because of the equalizing effect of the ongoing migration, only small and temporary differences between the slopes (0 – 0.06) were regarded by us as random fluctuations (drift). Three TEs were intermediate (0.08-0.09) and await additional research. The 11 TEs with large frequency differences (0.12 – 0.22) were regarded by us as putative adaptive TEs, because the equalizing power of ongoing migration will eliminate random large differences. Five of them were higher on the SFS and six were higher on the NFS. Gaps in the distribution of the differences distinguished between the large and small differences. The large gap among the 11 TEs favored on the NFS was  significant  and supports our rejection of drift as the only explanation of the distribution of the slope differences. The gaps in the distribution of the differences separated the putative TEs with strong enough selection from those TEs that couldn't overrule the migration.  The results are compared and contrasted with the directional effect of the frequencies of the same TEs in the study of global climatic comparisons across thousands of kilometers. From the 11 putative adaptive TEs in the local “Evolution Canyon,” six differentiate in the same direction as in the continental comparisons and four in the opposite direction. One TE, FBti0019144, differentiated in EC in  the same direction  as in Australia and in the  opposite direction  to that of North America.    Conclusions  We presume that the major divergent evolutionary driving force at the local EC microsite is natural selection overruling gene flow. Therefore, after we rejected drift as an explanation of all the large slope differences, we regarded them as  putatively adaptive . In order to substantiate the individual TE adaptation, we need to increase the sample sizes and reveal the significant adaptive TEs.  The comparison of  local  and  global  studies show only  partial  similarity in the adaptation of the TEs, because of the dryness of the ecologically tropical climate in EC, in contrast to the wet tropical climate in the global compared climates. Moreover, adaptation of a TE may be expressed only in part of the time and specific localities.    Reviewers  Reviewed by Eugene Koonin, Limsoon Wong and Fyodor Kondrashov. For the full reviews, please go to the Reviewers’ comments section.    Electronic supplementary material  The online version of this article (doi:10.1186/s13062-015-0074-5) contains supplementary material, which is available to authorized users.

Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at “Evolution Canyon”, Mount Carmel, Israel