Abstract
To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5′ imperfect copy at its downstream and a 3′ imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3′ and 5′ imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.
Highlights
Voucher-specimen KIZglgs1240 KIZglgs1241 KIZglgs1259 IOZ8837 IOZ8838 IOZ8839 IOZ8840 IOZ8841 IOZ8842 IOZ15553 IOZ16728 IOZ18697 IOZ19841 IOZ19897 IOZ19898
In our previous study on the complete mitochondrial genome of the yellow-browed tits (Sylviparus modestus)[25], we found a 117 bp tandem repeat which repeated twice in the Domain III of its mitochondrial control region
We discussed the potential evolutionary dynamics and the possible origin of this tandem repeat region by mapping the number of repeat unit in different individuals onto the phylogenetic relationships based on a combined datasets containing control region sequence and 4 more mitochondrial loci
Summary
Five loci were amplified from all 15 surveyed individuals, and the combined dataset was 5323 bp in length (1143 bp for cyt b, 1041 bp for ND2, 684 bp for atp6, 1213 bp for COI, and 1242 bp for control region), while 55 sites were variable and 20 sites were parsimony informative. According to the known complete control regions from Paridae, no long repeated regions were found Investigation of these known parid control regions revealed a 120–121 bp motif similar to the combined 3′ and 5′ im copy (referred to the sequence showed in Table 2 hereafter) of yellow-browed tits (Table S2). Character-mapping analysis based on the parsimony method indicated that most of the arrangement patterns had multiple origins among all surveyed individuals (Fig. 4), revealed extreme variation in the patterns of tandem repeats in the mitochondrial control region of yellow-browed tits. This result suggests that reversions among different patterns may occur frequently and that a arrangement pattern may have multiple origins
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