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An Analysis of the Phylogenetic Relationship of Thai Cervids Inferred from Nucleotide Sequences of Protein Kinase C Iota (PRKCI) Intron

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An Analysis of the Phylogenetic Relationship of Thai Cervids Inferred from Nucleotide Sequences of Protein Kinase C Iota (PRKCI) Intron Kasetsart J. (Nat. Sci.) 43 : 709 - 719 (2009) An Analysis of the Phylogenetic Relationship of Thai Cervids Inferred from Nucleotide Sequences of Protein Kinase C Iota (PRKCI) Intron Kanita Ouithavon1, Naris Bhumpakphan2, Jessada Denduangboripant3, Boripat Siriaroonrat4 and Savitr Trakulnaleamsai5* ABSTRACT The phylogenetic relationship of five Thai cervid species (n=21) and four spotted deer (Axis axis, n=4), was determined based on nucleotide sequences of the intron region of the protein kinase C iota (PRKCI) gene. Blood samples were collected from seven captive breeding centers in Thailand from which whole genomic DNA was extracted. Intron1 sequences of the PRKCI nuclear gene were amplified by a polymerase chain reaction, using L748 and U26 primers. Approximately 552 base pairs of all amplified fragments were analyzed using the neighbor-joining distance matrix method, and 19 parsimony- informative sites were analyzed using the maximum parsimony approach. Phylogenetic analyses using the subfamily Muntiacinae as outgroups for tree rooting indicated similar topologies for both phylogenetic trees, clearly showing a separation of three distinct genera of Thai cervids: Muntiacus, Cervus, and Axis. The study also found that a phylogenetic relationship within the genus Axis would be monophyletic if both spotted deer and hog deer were included. Hog deer have been conventionally classified in the genus Cervus (Cervus porcinus), but this finding supports a recommendation to reclassify hog deer in the genus Axis. Key words: Thailand, the family Cervidae, protein kinase C iota (PRKCI) intron, phylogenetic tree, taxonomy INTRODUCTION 1987; Gentry, 1994). Cervids, or what is commonly called “deer,” are mostly characterized The family Cervidae is one of the most by antlers with a bony inner core and velvet skin specious families of artiodactyls, with an extensive cover. Antlers are presented in males, except in morphological and ecological divergence (Grubb, Rangifer in which both sexes have antlers, and the 1993). The diversity of their terrestrial habitats is single species in the genus Hydropotes, which thought to reflect several adaptive radiations and lacks antlers (Lekagul and McNeely, 1977; their high level of homoplasy (Groves and Grubb, Nowak, 1999). In the classification of Janis and 1 Department of Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand. 2 Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand. 3 Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand. 4 The Zoological Park Organization under the Royal Patronage of His Majesty the King, Bangkok 10300, Thailand. 5 Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand. * Corresponding author, e-mail: [email protected] Received date : 20/03/09 Accepted date : 20/05/09 710 Kasetsart J. (Nat. Sci.) 43(4) Scott (1987), and Groves and Grubb (1987), traditionally used to resolve intra-subfamily Cervidae are classified into six subfamilies: relationships (Bubenik and Bubenik, 1990). These Muntiacinae, Cervinae, Alcinae, Rangiferinae, diagnostic characteristics either could be a Odocoileinae and Hydropotinae. The subfamily phylogenetically informative inheritance from Muntiacinae contains two Asian genera: their ancestors, or caused by a convergence due to Muntiacus and Elaphodus, and the subfamily ecological adaptations, which could represent Cervinae includes four genera: Dama, Axis, different ecomorphs (Geist, 1998; Grubb, 1993; Elaphurus and Cervus. Vrba and Schaller, 2000). Therefore, traditional According to the traditional classification classifications with merely morphological of Lekagul and McNeely (1977), which is based characteristics are still inadequate. on characteristics of antlers and skulls, there are Molecular phylogenetic investigations six species from two subfamilies (Muntiacinae and have greatly helped in taxonomical organization Cervinae) of Cervidae in Thailand. The subfamily and also to understand better the evolution of Muntiacinae in Thailand consists of common morphological characters. Several molecular barking deer (Muntiacus muntjak) and Fea’s studies on Cervidae have considerably contributed barking deer (Muntiacus feae). The subfamily to resolving the debate on evolutionary Cervinae consists of sambar deer (Cervus relationships among deer species based on amino unicolor), the extinct Schomburgk’s deer (Cervus acid, mitochondrial DNA and nuclear DNA shomburgki), Eld’s deer (Cervus eldii) and hog sequences (Miyamoto et al., 1990; Cronin et al., deer (Cervus porcinus). Lekagul and McNeely’s 1996; Douzery and Randi, 1997; Pitra et al., 2004; classification is different from many modern Gilbert et al., 2006). However, these previous authors who have placed hog deer in the genus studies did not have enough representative taxa Axis, based on the lack of upper canines, which of cervid species found in Thailand. Moreover, are variably present in other Cervus species and they did not properly clarify the taxonomy of Thai the presence of glands in the feet (Groves and deer due to the intergeneric relatedness between Grubb, 1987; Nowak, 1999). This contradiction genera within Cervidae. is one of many remaining inconsistencies Therefore, this study selected the nuclear concerning the morphological classifications of DNA intron region of the protein kinase C iota intergeneric relationships among the family gene (PRKCI), a neutral and rapidly evolving Cervidae. gene, as a molecular marker to analyze For the comparative morphology of phylogenetic relationships among Thai deer. This extant deer, the discrepancies between phylogenies study addressed two important phylogenetic of Cervidae can be explained by the fact that most questions by determining: (1) whether within the previous studies have used different matrices of subfamily Cervinae, the genera Cervus and Axis morphological characteristics (Groves and Grubb, are monophyletic; and (2) the location of the best 1987; Meijaard and Groves, 2004). It is very phylogenetic position of hog deer. difficult to appraise the reliability of their inferences because of the high level of homoplasy MATERIALS AND METHODS affecting these morphological characteristics. Consequently, the results from the decipherment Sample collection in the phylogeny of Cervidae have been repeatedly Blood samples were collected from five questioned (Janis and Scott, 1987; Gentry, 1994; species of Thai deer: hog deer (Cervus porcinus Hassanin and Douzery, 2003). Several dental and or Axis porcinus); sambar deer (C. unicolor); both cranial characters, especially those of antlers, were subspecies of Eld’s deer (Siamese Eld’s deer, C. Kasetsart J. (Nat. Sci.) 43(4) 711 eldii siamensis, and thamin Eld’s deer, C. eldii samples was extracted using an Aquapure thamin); common barking deer (Muntiacus Genomic Blood Kit (Bio-RAD). The extracted muntjak); and Fea’s barking deer (M. feae). DNA with a total volume of 100 µl of TE buffer Moreover, one additional species of Axis deer was stored at –20°C in a refrigerator. Each DNA (spotted deer, Axis axis) that is not native to extract was used as a template for PCR Thailand was included in the sample. All deer amplification, with the primer pair U26 and L748 specimens were sampled from seven zoos and from the previous study by Ropiquet and Hassanin captive breeding centers around Thailand. These (2005). PCR products of PRKCI intron were centers are operated by the Zoological Park amplified in a 15 µl reaction containing 1.5 µl of Organization under the Royal Patronage of His 10x Tag buffer, 1.5 µl of 2.5 mM MgCl2, 0.075 µl Majesty the King and by the Wildlife Propagation of Taq DNA polymerase (Fermentas), 1.2 µl of Division, Department of National Park, Wildlife 2.0 mM dNTP mixture and 0.75 µl of 5 pmol/µl and Plants Conservation (DNP). The sources of of each primer. The thermal cycling program each sample are shown in Table 1. The collected consisted of an initial denaturation step at 94°C blood samples in vacutainers were kept in ice while for 4 minutes, 35 cycles of a denaturation step at being transported to the laboratory at Kasetsart 94°C for 20 seconds, an annealing step at 53°C University. Then, they were kept cool at 4°C in a for 30 seconds, with an extension step at 72°C for refrigerator. 1 minute and a final extension step at 72°C for 5 minutes. The PCR products were then purified by Laboratory methodology hydrolysis of the primers with exonuclease I and Whole genomic DNA from the blood removal of phosphoric acid of dNTPs by alkaline Table 1 Names and number of deer samples used in the study. Common name Scientific name Sample name Source Number of sample Common barking Muntiacus M2, M3 Pattalung Wildlife Stationa 2 deer muntjak Fea’s barking Muntiacu feae F1, F2 Ton Nga-Chang Wildlife 2 deer Stationa Hog deer Cervus porcinus P1, P5, P6 Hauy Sai Wildlife Stationa 6 or Axis porcinus P9 Dusit Zoob P11 Korat Zoob P12 Songkhla Zoob Sambar deer Cervus unicolor U2, U3, U4, Hauy Sai Wildlife Stationa 5 U5 Songkhla Zoob U8 Khao Kho Wildlife Stationa Siamese Eld’s Cervus eldii S1 Dusit Zoob 1 deer siamensis Thamin Eld’s Cervus eldii T1, T2, T7 Hauy Sai Wildlife Stationa 5 deer thamin T9, T11 Dusit Zoob Spotted deer Axis axis A1, A2 Songkhla Zoob 4 A3, A4 Korat Zoob a = Wildlife Propagation Division, DNP b = The Zoological Park Organization under the Royal Patronage of His Majesty the King 712 Kasetsart J. (Nat. Sci.) 43(4) phosphatase using ExoSAP-IT (USB 552 aligned base sites of the amplified PRKCI Corporation, USA), with 1 µl of ExoSAP-IT gene intron sequences. Two types of phylogenetic added in each PCR product tube. The mixture had analyses were carried out to investigate genetic to be left at room temperature for 30 minutes relationships: (1) neighbor-joining (NJ) analysis; before being placed into the thermal cycler. The and (2) maximum parsimony (MP) analysis using standard conditions used for PCR purification PAUP* version 4.010b (Swofford, 2002). For the consisted of the first step at 37°C for 20 minutes NJ tree, non-parametric bootstrap analyzes with and the second step at 80°C for 15 minutes.
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