Nucleotide diversity of a ND5 fragment confirms that population expansion is the most suitable explanation for the mtDNA haplotype polymorphism of Drosophila subobscura

Abstract

Results from mitochondria (mt) DNA restriction site analyses (RSAs) have revealed that wild populations of Drosophila subobscura are formed by two common (I and II) and some rare, often endemic, low-frequency haplotypes. In the study reported here, we analysed nucleotide diversity in a 942-bp fragment of the mtDNA ND5 gene in 48 D. subobscura individuals captured from three populations that showed haplotypes I, II or the less common ones, as well as in one additional individual belonging to D. guanche that was taken as an outgroup. RSAs and sequencing results were compared. The two approaches yielded similar nucleotide variability parameters, suggesting a consistency in the results obtained from mtDNA dynamics in natural populations of D. subobscura. Patterns of polymorphism at ND5 are most consistent with the hypothesis of population expansion after a bottleneck that may have occurred since the last glaciation or which may occur seasonally after the summer and winter. However, we cannot rule out that selection has a role in maintaining the two major haplotypes at intermediate frequencies in worldwide populations of D. subobscura.

Gene expression clines reveal local adaptation and associated trade-offs at a continental scale

“…After that, samtools was used to combine per-sample bam files into a single mpileup file, which was then converted into the “sync” format associated with the PoPoolation2 package87. We identified the polymorphism in the mtDNA HaeIII cut site (“A” allele in our assembly) using sequence information provided in Castro et al 88. and calculated its frequency for each sample.…”

Within‐population genetic effects of mtDNA on metabolic rate in Drosophila subobscura

“…Within most populations, the two dominating mtDNA haplotypes (named I and II) occur at almost equal frequencies, whereas a number of population specific haplotypes are very rare (Castro et al ., ; Christie et al ., ; Jelic et al ., ). This pattern of mtDNA haplotype polymorphism is confirmed when analysing nucleotide sequence data from the mitochondrial ND5 gene rather than RSP (Castro et al ., ). Third, D. subobscura is a classic model system for studying how selection acts to maintain autosomal polymorphism (Balanyà et al ., ), and several previous studies collectively suggest that selection plays a role in the maintenance of mtDNA polymorphism in this species.…”

Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions

“…As suggested in previous studies and concordant with recovery from the last glaciations, the three models considered ( Fig. 1) incorporate changes in species size at different time intervals, and they all share a final population size expansion: (i) the expansion model (M1) is a simple stepwise expansion model (Rozas & Aguad e 1990; S anchez-Gracia & Rozas 2011); (ii) the bottleneck model (M2) is a simple stepwise reduction plus expansion model that incorporates the possible size changes due to past glacial periods (Castro et al 2010); and (iii) the admixture model (M3) is a bottleneck and subdivision model that incorporates the possible isolation in glacial refugia (Menozzi & Krimbas 1992).…”