Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels

Abstract

The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineage-specific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS < 1 in the concatenated protein-coding genes suggested purifying selection as driving force for shaping mitogenome diversity in camels. Additional analyses of the functional divergence in amino acid changes between species-specific lineages indicated fixed substitutions in various genes, with radical effects on the physicochemical properties of the protein products. The evolutionary time estimates revealed a divergence between domestic and wild Bactrian camels around 1.1 [0.58-1.8] million years ago (mya). This has major implications for the conservation and management of the critically endangered wild species, Camelus ferus.

Figure 1

Geographical locations of the samples used in this study, including three published mitogenomes obtained from GenBank. The size of each circle is proportional to the sample size for that location. Colors correspond to the three Old World camel species, and the number of individuals per species are shown within parentheses. Detailed sample information is given in Table S1. The map and figures are adopted from https://openclipart.org and are licensed under Creative Commons Zero 1.0 License.

Figure 2

The Maximum likelihood phylogenetic tree inferred from 11,379 bp concatenated protein-coding genes from 10 different species. The HKY substitution model with a gamma distribution and proportion of invariant sites (+GI) was used to model evolutionary rate differences. Lineage-specific dN/dS values for concatenated protein-coding genes are indicated in green over each branch. The estimated divergence time (mya; using first and second protein-coding positions) of each evolutionary lineage is shown in purple color, with confidence intervals in brackets. The statistical support for each node is based on 100 bootstrap replicates, with values (in black) on nodes indicating bootstrap supports above 50%; an asterisk indicates a value of 100%. Branch lengths are scaled as the number of base pair changes per site, with the exception of the human outgroup sequence which is rescaled for aesthetic purposes. The figures depicted on the phylogenetic tree are adopted from https://openclipart.org, and are licensed under Creative Commons Zero 1.0 License.