Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences

Nur Syafika Mohd-Yusof, Nik Abdul Rahman Nik-Rashidi, Nadiatur Akmar Zulkifli, Salmah Yaakop, Izfa Riza Hazmi, Badrul Munir Md. Zain

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

In Malaysia, stingless bee Heterotrigona itama is one of the bee species that is actively reared and mostly utilized in meliponiculture practice. In this preliminary study, we described the phylogenetic relationship scenario among selected localities of H. itama in Peninsular Malaysia and Borneo. Genomic DNA from 16 samples of five localities in Peninsular Malaysia (Kedah, Kelantan, Melaka and Johor) and Borneo (Sarawak) was successfully extracted and sequenced for phylogenetic analysis. The 489 bp mitochondrial DNA of COI sequences was generated for phylogenetic tree reconstruction and population genetic analysis. Tree topology indicated two monophyletic clades which belong to Peninsular Malaysia and Sarawak specimens with high bootstrap support. Five population genetic parameters were studied including nucleotide diversity (π), net nucleotide divergence (Da), nucleotide subdivision (Nst), population subdivision (FST) and gene flow (Nm). The Sarawak samples had the highest scores for all five parameters indicating its genetic affinity to the population in Peninsular Malaysia. Haplotype analysis showed that Kedah-Kelantan samples shared the same haplotype while Sarawak samples had its own unique haplotype with no sharing of haplotypes between other localities. Minimum-Spanning Network generated a visual representation of the relationship reflect a clear separation between Sarawak and Peninsular Malaysia stingless bees samples. This preliminary study shows the importance of understanding the systematic data towards conservation efforts of Malaysian stingless bee’s diversity.

Original languageEnglish
Pages (from-to)36-48
Number of pages13
JournalSerangga
Volume23
Issue number2 Special Issue
Publication statusPublished - 1 Jan 2018

Fingerprint

Borneo
bee
Malaysia
phylogenetics
nucleotide sequences
DNA
phylogeny
stingless bees
haplotypes
population genetics
nucleotides
genetic analysis
meliponiculture
mitochondrial DNA
topology
sampling
gene flow
genomics
divergence
founder effect

Keywords

  • COI
  • DNA barcode
  • Heterotrigona itama
  • Stingless bee

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Insect Science

Cite this

Mohd-Yusof, N. S., Nik-Rashidi, N. A. R., Zulkifli, N. A., Yaakop, S., Hazmi, I. R., & Md. Zain, B. M. (2018). Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences. Serangga, 23(2 Special Issue), 36-48.

Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences. / Mohd-Yusof, Nur Syafika; Nik-Rashidi, Nik Abdul Rahman; Zulkifli, Nadiatur Akmar; Yaakop, Salmah; Hazmi, Izfa Riza; Md. Zain, Badrul Munir.

In: Serangga, Vol. 23, No. 2 Special Issue, 01.01.2018, p. 36-48.

Research output: Contribution to journalArticle

Mohd-Yusof, NS, Nik-Rashidi, NAR, Zulkifli, NA, Yaakop, S, Hazmi, IR & Md. Zain, BM 2018, 'Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences', Serangga, vol. 23, no. 2 Special Issue, pp. 36-48.
Mohd-Yusof NS, Nik-Rashidi NAR, Zulkifli NA, Yaakop S, Hazmi IR, Md. Zain BM. Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences. Serangga. 2018 Jan 1;23(2 Special Issue):36-48.
Mohd-Yusof, Nur Syafika ; Nik-Rashidi, Nik Abdul Rahman ; Zulkifli, Nadiatur Akmar ; Yaakop, Salmah ; Hazmi, Izfa Riza ; Md. Zain, Badrul Munir. / Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences. In: Serangga. 2018 ; Vol. 23, No. 2 Special Issue. pp. 36-48.
@article{6a8592467a7c4d5c95323feaf2307585,
title = "Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences",
abstract = "In Malaysia, stingless bee Heterotrigona itama is one of the bee species that is actively reared and mostly utilized in meliponiculture practice. In this preliminary study, we described the phylogenetic relationship scenario among selected localities of H. itama in Peninsular Malaysia and Borneo. Genomic DNA from 16 samples of five localities in Peninsular Malaysia (Kedah, Kelantan, Melaka and Johor) and Borneo (Sarawak) was successfully extracted and sequenced for phylogenetic analysis. The 489 bp mitochondrial DNA of COI sequences was generated for phylogenetic tree reconstruction and population genetic analysis. Tree topology indicated two monophyletic clades which belong to Peninsular Malaysia and Sarawak specimens with high bootstrap support. Five population genetic parameters were studied including nucleotide diversity (π), net nucleotide divergence (Da), nucleotide subdivision (Nst), population subdivision (FST) and gene flow (Nm). The Sarawak samples had the highest scores for all five parameters indicating its genetic affinity to the population in Peninsular Malaysia. Haplotype analysis showed that Kedah-Kelantan samples shared the same haplotype while Sarawak samples had its own unique haplotype with no sharing of haplotypes between other localities. Minimum-Spanning Network generated a visual representation of the relationship reflect a clear separation between Sarawak and Peninsular Malaysia stingless bees samples. This preliminary study shows the importance of understanding the systematic data towards conservation efforts of Malaysian stingless bee’s diversity.",
keywords = "COI, DNA barcode, Heterotrigona itama, Stingless bee",
author = "Mohd-Yusof, {Nur Syafika} and Nik-Rashidi, {Nik Abdul Rahman} and Zulkifli, {Nadiatur Akmar} and Salmah Yaakop and Hazmi, {Izfa Riza} and {Md. Zain}, {Badrul Munir}",
year = "2018",
month = "1",
day = "1",
language = "English",
volume = "23",
pages = "36--48",
journal = "Serangga",
issn = "1394-5130",
publisher = "Universiti Kebangsaan Malaysia",
number = "2 Special Issue",

}

TY - JOUR

T1 - Phylogenetic relationships of heterotrigona itama in Malaysia based on COI DNA sequences

AU - Mohd-Yusof, Nur Syafika

AU - Nik-Rashidi, Nik Abdul Rahman

AU - Zulkifli, Nadiatur Akmar

AU - Yaakop, Salmah

AU - Hazmi, Izfa Riza

AU - Md. Zain, Badrul Munir

PY - 2018/1/1

Y1 - 2018/1/1

N2 - In Malaysia, stingless bee Heterotrigona itama is one of the bee species that is actively reared and mostly utilized in meliponiculture practice. In this preliminary study, we described the phylogenetic relationship scenario among selected localities of H. itama in Peninsular Malaysia and Borneo. Genomic DNA from 16 samples of five localities in Peninsular Malaysia (Kedah, Kelantan, Melaka and Johor) and Borneo (Sarawak) was successfully extracted and sequenced for phylogenetic analysis. The 489 bp mitochondrial DNA of COI sequences was generated for phylogenetic tree reconstruction and population genetic analysis. Tree topology indicated two monophyletic clades which belong to Peninsular Malaysia and Sarawak specimens with high bootstrap support. Five population genetic parameters were studied including nucleotide diversity (π), net nucleotide divergence (Da), nucleotide subdivision (Nst), population subdivision (FST) and gene flow (Nm). The Sarawak samples had the highest scores for all five parameters indicating its genetic affinity to the population in Peninsular Malaysia. Haplotype analysis showed that Kedah-Kelantan samples shared the same haplotype while Sarawak samples had its own unique haplotype with no sharing of haplotypes between other localities. Minimum-Spanning Network generated a visual representation of the relationship reflect a clear separation between Sarawak and Peninsular Malaysia stingless bees samples. This preliminary study shows the importance of understanding the systematic data towards conservation efforts of Malaysian stingless bee’s diversity.

AB - In Malaysia, stingless bee Heterotrigona itama is one of the bee species that is actively reared and mostly utilized in meliponiculture practice. In this preliminary study, we described the phylogenetic relationship scenario among selected localities of H. itama in Peninsular Malaysia and Borneo. Genomic DNA from 16 samples of five localities in Peninsular Malaysia (Kedah, Kelantan, Melaka and Johor) and Borneo (Sarawak) was successfully extracted and sequenced for phylogenetic analysis. The 489 bp mitochondrial DNA of COI sequences was generated for phylogenetic tree reconstruction and population genetic analysis. Tree topology indicated two monophyletic clades which belong to Peninsular Malaysia and Sarawak specimens with high bootstrap support. Five population genetic parameters were studied including nucleotide diversity (π), net nucleotide divergence (Da), nucleotide subdivision (Nst), population subdivision (FST) and gene flow (Nm). The Sarawak samples had the highest scores for all five parameters indicating its genetic affinity to the population in Peninsular Malaysia. Haplotype analysis showed that Kedah-Kelantan samples shared the same haplotype while Sarawak samples had its own unique haplotype with no sharing of haplotypes between other localities. Minimum-Spanning Network generated a visual representation of the relationship reflect a clear separation between Sarawak and Peninsular Malaysia stingless bees samples. This preliminary study shows the importance of understanding the systematic data towards conservation efforts of Malaysian stingless bee’s diversity.

KW - COI

KW - DNA barcode

KW - Heterotrigona itama

KW - Stingless bee

UR - http://www.scopus.com/inward/record.url?scp=85055713594&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85055713594&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:85055713594

VL - 23

SP - 36

EP - 48

JO - Serangga

JF - Serangga

SN - 1394-5130

IS - 2 Special Issue

ER -