Sequence Divergence and Phylogenetic Status of Four Species of Testudinidae Family

Research Article

Open Access

Bheem Dutt Joshi

Bheem Dutt Joshi, 10 mdda Colony Rajpur, Dehradun, India

^*Corresponding authors:

Bheem Dutt Joshi
10 mdda Colony Rajpur
Dehradun, India
E-mail: mahideep71@gmail.com

Received October 29, 2012; Published July 07, 2012

Citation: Joshi BD (2012) Sequence Divergence and Phylogenetic Status of Four Species of Testudinidae Family. 1: 145. doi:10.4172/scientificreports.145

Copyright: © 2012 Joshi BD. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Abstract

Phylogenetic study is most useful approach for understand the evolutionary history of the species. Sequence divergence and phylogenetic status of four turtle species was estimated and constructed using 12S rRNA mitochondrial gene, for the conservation and as well as in management plans of endangered species of turtle which is highly poached for the human consumption in nation and international trade. All the sequences were obtained from the NCBI, edited and aligned in BioEdit Software for the analysis. Phylogenetic tree and sequence divergence were made in MEGA 5 software package. Sequence divergence between the four turtle species were ranges from 0.021 to 0.064 and within the species was 0.0003 in T. horsfieldii, where as in rest of three species sequence divergence was 0.000. For the identification of species, species specific nucleotides were also reported in the four species of turtle.

Keywords

Turtle; mtDNA; PCR; Sequence divergence; Species specific Nucleotide; phylogeny

Introduction

Molecular phylogenetic analysis is more reliable method for build a phylogenetic trees than the particular other methods; these methods have been used by many authors [1,2]. Genetic comparisons are helpful to understand ancestry of related species at higher taxonomic levels. Consequential morphological characteristics can be difficult to determine ancient divergences of the species, [3-5]. Phylogenetic suggestion must consider the population processes that produced the gene tree by three methods, first methods applied by mathematical population genetic methods, by calculating the conditional probabilities of genealogies given different species trees or population histories [5-7] second, by estimating population genetic parameters using methods that incorporate into the analysis both the large variance inherent in the coalescent process as well as improbability about the genealogical reconstruction [8,9] and third, by calculating outline statistics that do not use the gene tree for parameter estimation [10,11] For instance, pairwise divergence time has been used to infer sister relationships among a group of taxa. 12S rRNA is highly conserved and applied to illustrate the phylogeny of higher categorical levels such as phyla or subphyla [12]. The aim of the present analysis is to provide a preliminary insight into the sequence divergence and phylogenetic status of four turtle species using 12S rRNA and can be used to find unique SNPs (single nucleotide polymorphism) for species identification.

Materials and Methods

All sequence data were obtained from GenBank on the NCBI website (https://www.ncbi.nlm.nih.gov/) for the comparisons of 12S rRNA gene, of four turtle species. Sequences were aligned using BioEdit software with Clustal W program. Sequence divergence and phylogenetic trees were constructed for 12S rRNA sequence alignments using the Maximum Parsimony in the Molecular Evolutionary Genetics Analysis (MEGA) software package version 5.0.

Result and Discussion

Based on the 12S rRNA analysis, sequence divergence in the all four turtle species viz., T. kleinmanni, T. marginata T. graeca graeca and T. horsfieldii were ranged from 0.021 to 0.064, whereas lower sequence divergence were between the T. kleinmanni and T. kleinmanni (0.021) and maximum divergence were between the T. graeca graeca and T. horsfieldii (0.064). Sequence divergence estimated within the four turtle species was (0.000) except T. horsfieldii (0.003) (Table 1). In this study nucleotide diversity in T. kleinmanni and T. graeca graeca were 0.00036 and 0.01020 respectively. In the T. graeca graeca nucleotide diversity estimated high rather than the T. kleinmanni. Nucleotide diversity was found less due to 12S rRNA is much conserved region and hence not suitable for to estimatation genetic diversity within the species but can be used for species identification.

Table 1: Sequence divergence of mitochondrial 12S rRNA between the turtle species of Testudinidae family.

Based on phylogenetic tree analysis, T. kleinmanni is very closer to the T. marginata with higher bootstrap value of 89 then the T. graeca graeca and T. horsfieldii having bootstrap value of 67 (Figure 1). Unique SNPs for species identification were observed at specific nucleotide positions in the four turtle species (Table 2). But in the species T. kleinmanni and T. marginata no species specific nucleotide were observed due to very closely related species or 12S r RNA have very conserved sequence in species.

Figure 1: Maximum parsimony (M-P) tree constructed of 12S rRNA with four turtle species.

Table 2: Species specific nucleotide position in 12S rRNA gene. Nucleotide positions are as the sequence of T. kleinmanni (Accession no. NC007699.1).

Acknowledgements

I would like extend great thank to the following Accession no. NC007699.1, DQ991958.1, DQ991957.1, DQ991956.1, DQ991955.1, DQ991954.1, DQ991953.1, DQ991952.1, DQ991951.1, DQ991950.1, DQ991949.1, DQ991948.1, DQ991947.1, DQ991946.1, DQ991945.1, AF175333.1, AM491031.1, DQ205434.1, DQ205433.1, EU263120.1, EU263113.1, AF175328.1, DQ445844.1 and AB090020.1.

References