Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers.

Watcharaporn Thapana,Syed Farhan Ahmad,Thitipong Panthum,Nararat Laopichienpong,Prateep Duengkae,Ekaphan Kraichak,Worapong Singchat,Nattakan Ariyaraphong,Kornsorn Srikulnath,Parinya Wongtienchai,Narongrit Muangmai

doi:10.3390/ani12020148

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers.

Watcharaporn Thapana, Syed Farhan Ahmad + Show 9 more

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https://doi.org/10.3390/ani12020148

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Abstract

Simple SummaryThe evolutionary patterns and phylogenetic utility of duplicate control regions (CRs) in 72 individuals of Varanus salvator macromaculatus and other varanids have been observed. Divergence of the two CRs from each individual revealed a pattern of independent evolution in CRs of varanid lineage. This study is a first step towards developing new phylogenetic evolutionary models of the varanid lineage, with accurate evolutionary inferences to provide basic insights into the biology of mitogenomes.Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

Highlights

IntroductionThe mitochondrial control region (mtCR) is a major noncoding segment of the vertebrate mitochondrial genome (mitogenome)
The mitochondrial control region is a major noncoding segment of the vertebrate mitochondrial genome
Variations in control regions (CRs) at the population and species level in varanids have not been fully elucidated [5,17]. In light of this scenario, we propose two hypotheses: (1) orthologous copies of duplicate CRs in different individuals are genetically similar due to independent evolution, or (2) two CRs (CR1 and CR2) as paralogous copies exhibit identical or highly similar nucleotide sequences from concerted evolution

Summary

Introduction

The mitochondrial control region (mtCR) is a major noncoding segment of the vertebrate mitochondrial genome (mitogenome). The nucleotide CR sequence is the most rapidly evolving region of the mitogenome, and it lacks coding sequences; it is widely used as a molecular marker in population genetics, phylogenetic studies, and phylogeographic studies [3,4,5]. Vertebrates such as birds, snakes, turtles, and fish exhibit segmental duplications within the CR or an entire duplication of the CR, leading to the formation of repeats or possible homogenization between the duplicated copies of CR [6,7,8].

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