Date

2015

Author

Akın Pekşen, Çiğdem

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Water frogs (genus Pelophylax) in the eastern Mediterranean region represent a genetically and phylogenetically diverse group. Their dependence on freshwater habitats makes them highly sensitive to geological and climatic changes. Thus they are an ideal group to study the effect of past geological processes on molecular evolution of protein-coding and non-coding genes on the genome and on patterns of phylogeography in the eastern Mediterranean region. In the first study, the complete sequence of water frog Pelophylax lessonae' serum albumin (SA) gene including all exons, all introns, upstream sequence of the 5' UTR and downstream sequence of the 3' UTR were reported. By aligning P. lessonae' albumin gene with albumin genes of closely and distantly related amphibian species, potential regulatory elements and functional motifs in the 5' UTR (TATA box, HP element, ADEI, ADEII) and 3' UTR (PLE, USE1 and 2, PAS, DSE), and in the exon-intron junctions were documented. Comparison of exon and intron lengths of the water frog with other vertebrate species revealed a strong length conservation in protein coding albumin exons among distinct vertebrate species, but high variation in intron lenghts. Moreover, the search of the entire scaffold for retroelements indicated several distinct classes of truncated retroelement families upstream of the 5' UTR, downstream of the 3' UTR and within individual albumin introns could be one of the important drivers of the albumin gene evolution. Finally, phylogenetic analysis based on nucleotide sequences of protein-coding albumin exons supported previous mitochondrial DNA (mtDNA) and the first intron of the SA gene findings which were the sister group relationship of P. lessonae and P. bergeri, a close relationships of P. ridibundus and P. cf. bedriagae from Anatolia. Moreover, P. epeiroticus is closely related to P. ridibundus/P. cf. bedriagae. In contrast to former mtDNA findings, the SA exon data revealed that P. shqipericus represent a distinct lineage, which was supported by previous protein electrophoretic investigations. In the second study, phylogeographic patterns between mitochondrial (ND2 and ND3) and nuclear markers (SAI-1+RanaCR1) for water frog complex of the eastern Mediterranean region were compared. On the basis of analysis using extensive data set from mtDNA and nuDNA markers, these markers revealed discordances in the tree topology, the number of genetic stocks, the level of genetic differentiation, the times of divergence and the patterns of geographic distribution among distinct water frog lineages. These discordances between two markers were discussed by distinct processes such as incomplete lineage sorting, retention of ancestral polymorphism, introgression after secondary contact reacting with sex-biased or adaptive processes, and distinct selective constraints on genes. The major water frog lineages in the eastern Mediterranean region, P. cretensis, P. cypriensis, the Levant (P. bedriagae), Cilician groups, Central Asia groups, and Anatolian main allele groups (MAGs) could be affected in distinct ways from these processes that were discussed in this study.

Subject Keywords

Pelophylax., Serum albumin., Molecular evolution.

URI

http://etd.lib.metu.edu.tr/upload/12618420/index.pdf
https://hdl.handle.net/11511/24325

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Graduate School of Natural and Applied Sciences, Thesis