Salmah Yaakop

Phylogenetic relationships of Malaysia's long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences.

Abstract Phylogenetic relationships among Malaysia’s long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo’s population was distinguished from Peninsula’s population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia’s M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations in Malaysia.

Continental monophyly and molecular divergence of Peninsular Malaysia's Macaca fascicularis fascicularis.

The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysias M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (F ST, Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysias population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysias M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations.

Molecular identification of blood meal sources of ticks (Acari, Ixodidae) using cytochrome b gene as a genetic marker

Abstract Blood meal analysis (BMA) from ticks allows for the identification of natural hosts of ticks (Acari: Ixodidae). The aim of this study is to identify the blood meal sources of field collected on-host ticks using PCR analysis. DNA of four genera of ticks was isolated and their cytochrome b (Cyt b) gene was amplified to identify host blood meals. A phylogenetic tree was constructed based on data of Cyt b sequences using Neighbor Joining (NJ) and Maximum Parsimony (MP) analysis using MEGA 5.05 for the clustering of hosts of tick species. Twenty out of 27 samples showed maximum similarity (99%) with GenBank sequences through a Basic Local Alignment Search Tool (BLAST) while 7 samples only showed a similarity range of between 91–98%. The phylogenetic trees showed that the blood meal samples were derived from small rodents (Leopoldamys sabanus, Rattus tiomanicus and Sundamys muelleri), shrews (Tupaia glis) and mammals (Tapirus indicus and Prionailurus bengalensis), supported by 82–88% bootstrap values. In this study, Cyt b gene as a molecular target produced reliable results and was very significant for the effective identification of ticks’ blood meal. The assay can be used as a tool for identifying unknown blood meals of field collected on-host ticks.

Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences

BackgroundThe chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus.ResultsPhylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consisting of N. ampullaria, N. mirabilis, N. gracilis and N. rafflesiana, and another containing both intermediately distributed species (N. albomarginata and N. benstonei) and four highland species (N. sanguinea, N. macfarlanei, N. ramispina and N. alba).ConclusionsThe trnL intron and ITS sequences proved to provide phylogenetic informative characters for deriving a phylogeny of Nepenthes species in Peninsular Malaysia. To our knowledge, this is the first molecular phylogenetic study of Nepenthes species occurring along an altitudinal gradient in Peninsular Malaysia.

Prevalence and evolutionary history of endosymbiont Wolbachia (Rickettsiales: Anaplasmataceae) in parasitoids (Hymenoptera: Braconidae) associated with Bactrocera fruit flies (Diptera: Tephritidae) infesting carambola

Wolbachia endosymbiont is a maternally inherited bacteria that infects a wide range of hosts, including parasitoids and their respective hosts. In this study, a total of 171 individuals of braconid endoparasitoids, consisting of Fopius arisanus, F. vandenboschi, Diachasmimorpha longicaudata, Psyttalia sp.1, Psyttalia sp.2, P. fletcheri and P. incisi, and their host tephritid fruit flies of Bactrocera dorsalis, B. papayae and B. carambolae infesting carambola were screened molecularly by the Wolbachia surface protein (wsp) gene. Interestingly, 21 (24.14%) wsp gene sequences were successfully isolated from 87 braconid samples tested, showing a low infection rate of Wolbachia. However, despite the close ecological contact between parasitoids and their hosts, none of the tephritid individuals were infected by Wolbachia. A comparison of wsp and host mitochondrial cytochrome c oxidase subunit I (COI) sequences found that braconids did not cluster in connection with Wolbachia infection, suggesting that selective sweep has not yet occurred because Wolbachia may have recently infected the braconid populations in Peninsular Malaysia (≈0.1 MYA). Despite of relatively recent infections of Wolbachia, the history of Wolbachia infection into F. arisanus populations of Peninsular Malaysia is complex, involving at least two independent occasions of infection and two secondary losses.

Phylogeny of economically important insect pests that infesting several crops species in Malaysia

This paper reported molecular data on insect pests of commercial crops in Peninsular Malaysia. Fifteen insect pests (Metisa plana, Calliteara horsefeldii, Cotesia vestalis, Bactrocera papayae, Bactrocera carambolae, Bactrocera latifrons, Conopomorpha cramella, Sesamia inferens, Chilo polychrysa, Rhynchophorus vulneratus, and Rhynchophorus ferrugineus) of nine crops were sampled (oil palm, coconut, paddy, cocoa, starfruit, angled loofah, guava, chili and mustard) and also four species that belong to the ferns pest (Herpetogramma platycapna) and storage and rice pests (Tribolium castaneum, Oryzaephilus surinamensis and Cadra cautella). The presented phylogeny summarized the initial phylogenetic hypothesis, which concerning by implementation of the economically important insect pests. In this paper, phylogenetic relationships among 39 individuals of 15 species that belonging to three orders under 12 genera were inferred from DNA sequences of mitochondrial marker, cytochrome oxidase subunit I (COI) and nuclear marker, ribosomal DNA 28S D2 region. The phylogenies resulted from the phylogenetic analyses of both genes are relatively similar, but differ in the sequence of evolution. Interestingly, this most recent molecular data of COI sequences data by using Bayesian Inference analysis resulted a more-resolved phylogeny that corroborated with traditional hypotheses of holometabolan relationships based on traditional hypotheses of holometabolan relationships and most of recently molecular study compared to 28S sequences. This finding provides the information on relationships of pests species, which infested several crops in Malaysia and also estimation on Holometabolas order relationships. The identification of the larval stages of insect pests could be done accurately, without waiting the emergence of adults and supported by the phylogenetic tree.

A preliminary study on activity budget, daily travel distance and feeding behaviour of long-tailed macaques and spectacled dusky leaf monkey in Bangi campus of Universiti Kebangsaan Malaysia, Selangor

The activity budget, ranging behaviour and feeding behaviour of a multimale-multifemale group of long-tailed macaques (Macaca fascicularis) and a multimale-multifemale group of spectacled dusky leaf monkey (Trachypithecus obscurus) were studied. A total of 145 hours and 143 hours have been spent to observe the group of long-tailed macaque and spectacled dusky leaf monkey that ranged the same habitat adjacent to the campus areas. The researchers examined the activity budgets, daily travel length and feeding activity of both species and distinguished how the sympatric species used the same forested habitat. Preliminary study found that the long-tailed macaques spent longer time feeding, moving than resting and other activities. On the other hand, the dusky leaf monkey spent much time in feeding and resting than moving. The differences of daily pattern between these two groups are significant. Macaques have higher daily mean of path length compared to the dusky leaf monkey and spent much time moving compare ...

Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker

Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variat...

The effect of different trap height on the diversity of sap beetle (Coleoptera: Nitidulidae)

This paper aim to measure the diversity and abundance of sap beetles in oil palm plantation in Malaysia on different heights, 1.5m and 2.5m above ground. A total 0f 20 baited traps were set up in Felda Lui Muda, Negeri Sembilan and located along three transects. The sap beetles collected weekly for a month and identified until species level and the diversity indexes were measured using Evenness Index (E), Shannon-Wiener Index (H’), Simpson’s Index (D’) and Margalef’s Index (R’). All the diversity indexes indicated that the diversity on the lower height above the ground is higher than the upper height The result also shows that there are significant difference (p<0.05) when tested with t-test between the numbers of individuals on the different trap height although the number of species shows different results.

The effectiveness of 28S and 16S molecular regions in resolving phylogeny of Malaysian microgastrinae (Hymenoptera: Braconidae)

The phylogenetic relationships of Microgastrinae remains unclear though some studies have been conducted to resolve it. The function of Microgastrinae as endoparasitoids of Lepidopteran larvae makes this subfamily an ideal and potential species to be applied as biological control agent of infesting crops. In this study, a total of 13 microgastrine samples under 13 genera were collected from nine localities throughout Peninsular Malaysia. Two molecular regions, 28S nuclear marker and 16S mitochondrial marker were utilized in this study to examine the effectiveness of those regions in resolving the relationships within Microgastrinae. Total of 36 sequences were implemented in the analyses of NJ, MP and Bayesian for both markers. Results obtained from this study were supported by morphological and biological characters. Henceforth, the outcome from this study provides a proof of effectiveness of 28S and 16S molecular markers in studying the phylogenetic relationships of Microgastrinae from Malaysia exclusively and Oriental generally.The phylogenetic relationships of Microgastrinae remains unclear though some studies have been conducted to resolve it. The function of Microgastrinae as endoparasitoids of Lepidopteran larvae makes this subfamily an ideal and potential species to be applied as biological control agent of infesting crops. In this study, a total of 13 microgastrine samples under 13 genera were collected from nine localities throughout Peninsular Malaysia. Two molecular regions, 28S nuclear marker and 16S mitochondrial marker were utilized in this study to examine the effectiveness of those regions in resolving the relationships within Microgastrinae. Total of 36 sequences were implemented in the analyses of NJ, MP and Bayesian for both markers. Results obtained from this study were supported by morphological and biological characters. Henceforth, the outcome from this study provides a proof of effectiveness of 28S and 16S molecular markers in studying the phylogenetic relationships of Microgastrinae from Malaysia exclusive...