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TETRAGONULA MINANGKABAU and OTHER SPECIES USING CYTOCHROME B GENE Buti Y

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TETRAGONULA MINANGKABAU and OTHER SPECIES USING CYTOCHROME B GENE Buti Y DOI 10.2478/JAS-2019-0008 J. APIC. SCI. VOL. 63 NO. 1 2019J. APIC. SCI. Vol. 63 No. 1 2019 Original Article PHYLOGENETIC ANALYSIS OF TETRAGONULA MINANGKABAU AND OTHER SPECIES USING CYTOCHROME B GENE Buti Y. Christy* Dewi I. Roesma Dahelmi Biology Department, Faculty of Mathematic and Natural Science, Andalas University, Padang, Indonesia *corresponding author: [email protected] Received: 01 August 2018;accepted: 03 March 2019 Abstract Tetragonula a genus in the Meliponini tribe (Apidae), is difficult to identify due to the many cryptic species. As technology develops, molecular taxonomic studies are used to help identify species with limited morphological characteristics. This study presents an analysis of the phylogenetic relationship between several species in the Tetragonula ge- nus based on the sequences of the cytochrome b gene. Maximum parsimony, neighbor joining, maximum likelihood and minimum evolution methods were used to construct phylogenetic trees. The sequence divergence between T. minangkabau collected from Limau Manis and Ulu Gadut is 0.8%, while between T. minangkabau with T. minangkabau forma darek 5.5%. The low sequence divergence indicated that T. minangkabau and T. minangkabau forma darek have a close phylogenetic relationship. The analysis showed that Tetragonula (T. minangkabau, T. minangkabau forma darek, T. laeviceps, T. drescheri and T. fuscobalteata) is monophyletic. A sequence divergence of 5.5% supports the sepa- ration of Tetragonula minangkabau and T. minangkabau forma darek. Keywords: cytochrome b, phylogenetic analysis, Tetragonula, Tetragonula minangkabau INTRODUCTION Inoue (1985) revealed one species in Sumatra belonging to the Tetragonula laeviceps group Stingless bees are included in the family Apidae, with a smaller size and paler body parts compared Meliponini tribe and represent a group of cos- to the typical T. laeviceps. Due to these mor- mopolitan bees that can be found in the tropics phological differences, this species was named (O’Toole & Raw, 1991). From the taxonomic Tetragonula minangkabau (Sakagami & Inoue, aspect, various publications reported the dif- 1985), named after Minangkabau, which is the ferences in the number of species in Meliponini name of the ethnic community that inhabits the tribe. This is due to the large number of West Sumatra region. In the same year, Sakagami taxonomic revisions and cryptic species. There and Inoue also found two groups in the collected are over 374 species of stingless bees which T. minangkabau specimens that differed in head are divided into twenty-six genera (Michener, width and hind tibia length. The data obtained 2007). Another source states that members showed that the size of specimens from Lubuk of the Meliponini tribe are more than thirty- Minturun and other locations in West Sumatra three genera and 397 species (Moure, Urban, (generally from the highlands) differed sig- & Melo, 2007). Cortopassi-Laurino et al. (2006) nificantly. Specimens found in the highlands state that more than 600 stingless bee species were larger and possessed bigger hind legs belonging to fifty-six genera have been found and paler colored metasomas. This group of worldwide. Among them, 400 species are found specimens was named Tetragonula minangka- in the Neotropic region and at least forty-five bau forma darek. According to Braby, Eastwood species are found in Southeast Asia. & Murray (2012) forma is one of intraspesific In Indonesia and especially Sumatra, there has unit (beside varieties and races) which is not been research on the etho-ecological aspects formally recognized under ICZN (International of stingless bee since 1980. Sakagami and Code of Zoological Nomenclature). The name 117 Christy et AL. Phylogenetic analysis of Tetragonula minangkabau “darek” was proposed for the larger form as it bee) genus. means “highlands”, used especially in reference From the differences in body length and to the Bukittinggi area (Sakagami & Inoue, 1985; coloration, we hypothesised that T. minangkabau Sakagami, Inoue, & Salmah, 1990). Neverthe- forma darek can be classified as a different less, the taxonomic position of this form is still species from T. minangkabau. The purpose of unclear. this study was to analyze the phylogenetic Molecular markers have been used in many relationship among Tetragonula minangkabau, studies related to the stingless bee, including T. minangkabau forma darek and several species population, taxonomy and phylogenetic in the Tetragonula genus. inference. The use of molecular markers to determine the status of a taxa has been carried METHODS out in Liotrigona spp. using the COI gene (Koch, 2010) and nine Amazonian stingless bees using Stingless bee samples were collected directly 16S rRNA and COI with the PCR-SSCP technique with the use of insect nets and tweezers at (Souza & Carvalho-Zilse, 2014). Thummajit- the nest entrance. Ten individuals from each sakul et al. (2014) have studied the population colony were collected and preserved in alcohol. structure of Tetragonula pagdeni in Thailand Such specific characteristics from samples using the cytochrome b gene and ATPase6- obtained as body coloration, shape and color tRNAASP. Rasmussen and Cameron (2007) of the nest entrance were noted and pho- used mitochondrial genes (16S rRNA) and core tographed as supporting data for identifica- genes (nuclear long-wavelength rhodopsin copy tion. In sample collection and identification we I, elongation factor-1α copy F2 and arginine followed Sakagami, Inoue and Salmah’s method- kinase) to prove the non-monophyletic nature ology (1990). The locations of the Tetragonula of the genus Trigona sensu lato. Ramirez et al. sample collection is shown in Tab. 1. All the (2010) have conducted phylogenetic relation- samples obtained were used for the identifica- ship studies of the stingless bee for the genus tion process but only one individual from each Melipona using different fragments including colony was analyzed molecularly. mitochondrial CO1, ribosomal 16S, nuclear EF1-a, DNA isolation was performed according to the ArgK and Pol-II. Among examples of molecular INVITRO GEN PureLinkTM Genomic DNA Mini Kit studies on bees other than the Meliponini, protocol. Isolated DNA was visualized through Koulianos and Schmid-Hempel (2000) conducted the electrophoresis process on 1.2% agarose a study that used the cytochrome b and COI gel. Electrophoresis was performed at a voltage genes to determine the phylogenetic relation- of 100 mV for thirty-five minutes. The gel was ship of nineteen species in the Bombus (bumble then placed on top of the UV illuminator (GelDoc) Table 1. Location of Tetragonula sample collection Species Location Altitude (meters above sea level) Limau Manis 210 Tetragonula minangkabau Ulu Gadut 500 T. minangkabau forma darek Solok 1500 Limau Manis 255 T. fuscobalteata Sijunjung 220 T. laeviceps Malaysia 54 T. drescheri Malaysia 54 T. minangkabau Malaysia 54 118 J. APIC. SCI. Vol. 63 No. 1 2019 Table 2. List of species from NCBI GenBank used for construction of phylogenetic trees based on cytochrome b gene Accession No. Species Location number 1 Trigona clypearis AY575083 Australia (a) 2 Trigona laeviceps AY575080 Thailand (a) 3 Trigona collina AY575081 Thailand (a) 4 Tetragonula pagdeni FJ012146 Thailand (b) Annotation: (a) Franck et al. (2004); (b) Thummajitsakul et al. (2008) and the visualization results were documented. of the sequences obtained with sequences of DNA amplification was performed using the genes listed in the public database using the SensoQuest PCR machine. The PCR solution BLAST (Basic Local Alignment Search Tool) contained 1x reaction buffer (GoTaq® Green program which is done online via the NCBI’s Master Mix, Promega), 0.8 μM forward primer, National Center of Biotechnology Information 0.8 μM reverse primer, < 250 ng DNA template website: http://www.ncbi.nlm.nih.gov/BLAST. and nuclease freewater (DD H2O), which were Sequences of cytochrome b genes were aligned added to the total volume of 25 μl inside the PCR with data from GenBank (Tab. 2) with the use tube. The process of cytochrome gene amplifi- of the ClustalX program version 2.1 (Larkin et cation resulted in 600 bp fragment using cytb-F al., 2007). The alignment results were edited and cytb-R primers: TTCACTATATTATAAAA- manually using the BioEdit program (Hall, 1999). GATGTAAGTTC and: GGCAAAAAGAAAATAT- Furthermore, the sequences were converted CATTCAGG, respectively (Thummajitsakul et into the FASTA format (.fas) for the analysis of al., 2014). The PCR thermal profile consisted of the nucleotide variation. initial denaturation at 95°C for three minutes, Phylogenetic analysis based on DNA sequences followed by five cycles at 94°C for 30 seconds, of the partial cytochrome b gene was performed 42°C for 30 seconds and 72°C for 50 seconds. using the MEGA6 program (Tamura et al., 2013). Thirty-five cycles were then performed at 94°C Phylogenetic trees were constructed separately for thirty seconds, 58°C for thirty seconds and for cytochrome b genes using the Neighbour 72°C for fifty seconds. Post-elongation was Joining (NJ) analysis. Phylogenetic tree construc- done at 72°C for seven minutes. tion was also done for Maximum Likelihood (ML), The amplified DNA was visualized through the Minimum Evolution (ME) and Maximum Parsimony electrophoresis process using 2% agarose gel. (MP) methods with bootstrap 1000 replications. The Thermo Scientific GeneRuler 100 bp DNA The value of the divergence sequence was Ladder was used for sizing the DNA. Electro- obtained using the Kimura 2-Parameter model. phoresis was performed at a voltage of 100 mV The ingroup used in this research can be seen for 35 min. The gel was then placed on top of in Tab. 2. The outgroup used in this research the UV illuminator (GelDoc) and the visualization were Apis cerana (EF467437) and Bombus hy- results were documented. The DNA amplifica- perboreus (AF066968). tion results were sent to the sequence service companies (Lab MacroGen USA DNA Sequencing) RESULTS in South Korea. Forward and reverse DNA sequences were The GenBank accession numbers for these assembled to obtain DNA sequences with the sequences are as follows: T. fuscobaltea- use of the STAR DNA program (Seqman).
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