Papers by Rovie-Ryan Jeffrine J
Two captive giant pandas (Ailuropoda melanoleuca) were observed for nutritional preferences over ... more Two captive giant pandas (Ailuropoda melanoleuca) were observed for nutritional preferences over a period of seven months from 21st May until 31st December 2014 at the Zoo Negara Malaysia. Nutritional analyses were conducted on six local bamboo species which were fed to both pandas. It is evident in the present study that they prefer the culms of Dendrocalamus asper followed by culms of Bambusa vulgaris and bamboo leaves from Dendrocalamus asper, Bambusa vulgaris f. waminii and Thyrsostachys seamensis. Their preferences towards these local bamboo species correspond to the different nutrient values which contained high fibre in the culms and high protein and fat in the leaves. The overall feeding behaviour were well established and the growth performances were satisfactory suggesting that they have successfully adapted to the feeding regime. The pandas were observed to be in good health, active and alert with these bamboo diets throughout the study period.
Understanding the genetic variation of the Plasmodium parasites could play an important
role in c... more Understanding the genetic variation of the Plasmodium parasites could play an important
role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR)
markers have successfully been tested for investigating the genetic diversity of malaria
vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic
variation of Plasmodium species, as well. To illustrate the genetic diversity of two
infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium
cynomolgi, infected and uninfected monkey blood samples were separately collected on
filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic
ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis
of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of
three clusters. However, the most significant result of the cluster analysis was revealing
the high efficiency of ISSR markers in the discrimination of the two Plasmodium species
from each other. The cluster analysis showed a wide range of genetic diversity among both
Plasmodium and the long-tailed Macaque accessions. The principal component analysis
(PCA) also confirmed the cluster analysis results.
We examined the genetic diversity of 64 long-tailed macaques from the northern states of Peninsul... more We examined the genetic diversity of 64 long-tailed macaques from the northern states of Peninsular Malaysia covering the states of Perlis and Kedah including the Langkawi Island using the complete control region (CR) segment of the mitochondrial DNA. Standard genetic diversity including nucleotide diversity, haplotype diversity and genetic divergence were calculated. Moderate nucleotide diversity (π = 0.021) was observed which is higher than a previous study on the Penang M. fascicularis population. Twenty-three haplotypes were detected with haplotype diversity, h of 0.936. Haplotype sharing was observed among Langkawi and Perlis macaques indicating historical connection between the island and the mainland. Phylogenetic trees constructed grouped the samples into 4 groups without any obvious populations structuring.
The genetic diversity of the long-tailed macaques (Macaca fascicularis) from Penang, Malaysia, in... more The genetic diversity of the long-tailed macaques (Macaca fascicularis) from Penang, Malaysia, including Jerejak Island and the mainland area of the state of Penang, Seberang Perai were examined using 1,042 bp control region (CR) segment of the mitochondrial DNA (mtDNA). Twenty haplotypes were described with a single haplotype sharing between the mainland and the island which suggests that it is a remnant of the genetic makeup from the mainland. Compared to previous studies based on the CR, all the Penang haplotypes are newly described with none shared with the other regional populations of M. fascicularis. A single deletion mutation unique to the Penang samples (Groups I and II) could be a good indicator for the conservation of the genetic uniqueness and possibly should be managed as a management unit (MU). A summarised phylogenetic tree (NJ, MP, ML and Bayesian) supports the monophyletic clustering of the M. fascicularis as described in previous studies. The topology separates the Penang haplotypes into three major groups, which generally corresponds to their geographical distribution. We also noted that the Penang haplotypes are of the continental lineage which separated from the insular lineage at around 1.04 mya. Finally, we showed that the CR of the mtDNA is powerful and suitable for the quantification of intraspecific diversity in M. fascicularis.
DNA sequencing of the Y-chromosome testis-specific protein locus (TSPY) and sex-determining regio... more DNA sequencing of the Y-chromosome testis-specific protein locus (TSPY) and sex-determining region (SRY) was conducted on 27 Macaca fascicularis individuals from eight insular and two peninsula localities of Penang State, Malaysia. Five haplotypes were discovered from the Penang samples, of which four were unique for that population. These haplotypes constituted of related individuals as observed in the Y-chromosomal gene flow within and between the insular and mainland regions. The occurrence of a dominant haplotype shared amongst M. fascicularis from southern Thailand, the Malay Peninsula, and Sumatra could be the result of a recent dispersal event from the common Pleistocene refugia, which had most likely been located in the Malay Peninsula. A combination of nucleotides at 12 sites distinguished the M. fascicularis from the northern region of the Isthmus of Kra from those of the southern region including our samples. The molecular phylogenetic tree confirmed that, unlike conspecific populations from regions north of the Isthmus of Kra, M. fascicularis from the southern region of the isthmus were free of introgression of Y-chromosome from M. mulatta. We dated the last common ancestors shared by the fascicularis group at approximately 1.5 million years ago (mya). Also, we estimated the bifurcation between the insular and the continental lineages of M. fascicularis as approximately 0.7 mya, which had been estimated as 0.4 mya in a previous study. Finally, similarly to the observations on various taxa by previous authors we recognise the role of the Isthmus of Kra area as a genetic barrier to the dispersal of and to gene flow in M. fascicularis.
Objective: To demonstrate a noninvasive large mammalian genetic sampling method using blood meal ... more Objective: To demonstrate a noninvasive large mammalian genetic sampling method using blood meal obtained from a tabanid fly. Methods: Blood meal was recovered from the abdomen of an engorged tabanid fly (Haematopota sp.) which was captured immediately after biting a Sumatran rhino in captivity. The blood was applied on to a Whatman FTA襅blood card. Subsequent laboratory work was conducted to extract, amplify and sequence the DNA from the sample. Validation was done by sampling the hair follicles and blood samples from the rhinoceros and subjecting it to the same laboratory process. Results: BLAST search and
constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. Conclusions: This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases.
We report the development of a fast and reliable PCR-based method for sex identification of tiger... more We report the development of a fast and reliable PCR-based method for sex identification of tiger DNA designed to be incorporated into fluorescent short tandem repeat (STR) profiling. A single primer pair, consisting of a fluorescently-labelled forward primer and an unlabelled reverse primer, is used to co-amplify homologous fragments of a zinc finger (ZF) protein intron which exhibits size polymorphism between the X and Y chromosomes. The ZFX and ZFY amplicons differ in size by 12 bp and can thus be differentiated by capillary electrophoresis.
Comparison of 321 bp long mtDNA cytochrome b sequences of wild and captive Malayan tapir (Tapirus... more Comparison of 321 bp long mtDNA cytochrome b sequences of wild and captive Malayan tapir (Tapirus indicus)revealed low variation among the individuals investigated. Phylogenetic analyses using distance (neighbor-joining) analysis supported the monophyletic status of the Malayan tapir. Two haplotypes were identified out of 13 Malayan tapir analyzed.
This study was conducted from the 9th until 16th November 2003. A total of 31 fish from six local... more This study was conducted from the 9th until 16th November 2003. A total of 31 fish from six localities throughout Sabah were sampled. It was found that at least four forms of Hampala inhibit the Sabah river system. The widely spread form, H. macrolepidota and the Bornean endemic form, H. bimaculata was recorded on the west coast region of Sabah. The Sabah endemic form, H. sabana dominated the central eastern region of Sabah. The south eastern region demonstrates the existence of two forms distinctly different by their number of gill rakers: (1) Tawau population (gill raker counts: 10-11) and Kalabakan population (gill raker counts: 12-13). The Kalabakan form could possibly be a crytic species.
Sampling trips were done on the 22nd until 27th April 2006 and on the 14th until 17th June 2006 f... more Sampling trips were done on the 22nd until 27th April 2006 and on the 14th until 17th June 2006 for Sungai Tembat (ST) in Tembat Forest Reserve and Sungai Ketiar (SK), located at Hulu Terengganu, Terengganu, respectively. Cast net, gill net, and rod and line were deployed during both trips. A total of 219 specimens representing four orders, eight families and 22 species of fishes were caught. A total of 20 species were recorded for ST while only nine species were caught at SK during the study.
The museum fish collection has a total of 437 specimens of freshwater fishes from 13 orders and 4... more The museum fish collection has a total of 437 specimens of freshwater fishes from 13 orders and 41 families. A total of 76 valid species was listed, encompasses of 16.5% and 24.9% of the total fish species known to Malaysia and Peninsular Malaysia, respectively. 70 species are native to Malaysia, three are introduced (Barbonymus gonionotus, Oreochromis mossambicus, and Betta splendens), and one reintroduced (Trichogaster pectoralis). Clarias batu is listed as endemic while the native status of two species (Coilia nasus and Mystus vittatus) is questionable as both species are not listed as indigenous to Malaysia
The Sarawak …, Jan 1, 2007
wo separate assessments on bats diversity wefe conducted in Bako National Park for 12 trapping-ni... more wo separate assessments on bats diversity wefe conducted in Bako National Park for 12 trapping-nights. Our first a(sessmenl was condu( lell lrom d to lZ l(brudr) ZUU-\ followed by the secood assessment from 28'h August to 3'd September 2005. A total ol295 individuals from 22 species ofbats were captured using mist-nets and harp rraps during the suney, which accumulated to 226 trapping-nights. Hippotidert cemin r was recorded as the most abundance species with 30.8J% of total captures. A total of eight new records ofbats have been added to this park: Emballonara ma ti,la, Rhin1laph$ ltxut, Hippoidens ater, Hippotiderot bialor, Mloth maicola, Mjoti atet, Pipitrellat undermanni and Kerir,,oula pellacida. 'With tl,ese additional records, there are now at ieast 34 species ofbats known to occur in Bako National Park. A complete and long term study coveririg other areas oot included io this study would definitely increase bats diversity found in this park.
Pertanika Journal of …, Jan 1, 2006
Kajian ini telah dijalankan untuk mengkaji struktur populasi dan taksonomi Tor douronensis, sejen... more Kajian ini telah dijalankan untuk mengkaji struktur populasi dan taksonomi Tor douronensis, sejenis ikan air tawar tempatan yang penting di Malaysia Borneo, menggunakan analisis penjujukan 466 pasangan bes gen mitokondria sitokrom c oksides I (COl). Sejumlah 62 ekor sampel ikan telah diperoleh dari lima lokasi di Sarawak (N=53) dan Sabah (N=8). Analisis filogenetik menggunakan kaedah "NeighbourJoining" (N]) menyokong status monofiletik di antara'T. douronensis dan Tor tambroides; seterusnya mengukuhkan lagi status taksonomi keduaduanya sebagai spesies yang berlainan. Haplotaip T. douronensis seterusnya boleh dibahagikan kepada tiga kumpulan yang utama, dengan ikan Pelian dari Sabah membentuk kumpulannya sendiri (Kluster Ill) dengan sokongan (bootstrap) statistik yang kuat. Perbezaan genetik yang tinggi di antara haplotaip-haplotaip dari Sabah dengan Sarawak menunjukkan bahawa ikan Pelian Sabah mungkin merupakan sejenis spesies kriptik. Kajian ini menunjukkan variasivariasi intra dan inter-po-pulasi yang tinggi dalam T. douronensis. Variasi dalam kalangan sampel dalam populasi dijumpai di dalam kesemua populasiT. douronensis kecuali di dalam populasi Bario. Kehadiran perbezaan-perbezaan haplotaip yang tetap (unik) bersamaan dengan nilai F ST yang tinggi antara populasi-populasi T. douronensis, menyokong kesimpulan bahawa sedikit atau tiada migrasi berlaku di antara populasi-populasi yang dipisahkan oleh jarak geografi yangjauh atau sistem sungai yang berlainan. Walau bagaimanapun, perkongsian beberapa haplotaip antara populasi-populasi tersebut, contohnya antam Batang Ai dan Bario (HS6) dan antara Batang Ai dan Ulu Limbang/Ba Kelalan (HS2) memberi bukti yang T. douronensis mempunyai taburan yang meluas di kawasan tersebut di masa lalu, terutama semasa zaman Q:.taternary. Keseluruhannya, kajian ini berjaya memberikan maklumatmakluat yang berguna tentang struktur populasi dan taksonomi ikan T. douronensis di Malaysia Borneo. ABSTRACT This study examines the population structure and taxonomy ofTor douronensis, an important indigenousfreshwater fish species in Malaysian Borneo, by using sequence analysis of 466 base pairs of the mitochondrial cytochrome c oxidase I (COl) gene. A total of62fish samples were collected from five locations in Sarawak (N=54) and Sabah (N=8). The phylogenetic analysis using the NeighbourJoining (N]) method supported the monophyletic status between T. douronensis and Tor tambroides, which further reinforced their taxonomic status as distinct species. The T. douronensis haplotypes were further divided into three major groups, with the Pelian[uh from Sabah forming its own group (Cluster Ill) with strong bootstrap support. The large genetic differences separating the Sabah haplotypesfrom its Sarawak congeners suggested that the Pelian fish might represent a cryptic species. The current study showed high levels of intra and inter-population variations in T. douronensis. Within all population variations, T. douronensis populations were found, except in Bario. The presence offixed haplotype differences along with high F ST values among the populations ofT. douronensis, support the conclusion that little or no migration occurred among the extant YUZINE ESA ET AL.
… J. Trop. Agric. Sci, Jan 1, 2012
Zool Stud, Jan 1, 2008
In this study, we examined the genetic structure of Tor tambroides Valenciennes, an important ind... more In this study, we examined the genetic structure of Tor tambroides Valenciennes, an important indigenous freshwater fish species in Malaysia, using sequence analysis of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. In total, 92 T. tambroides samples were analyzed from 4 locations on Peninsular Malaysia (n = 87) and a single population from Sarawak (Batang Ai, n = 5) on Borneo I., and 4 sequences of Tor douronensis from Sarawak were used for comparisons. In total, 9 haplotypes were found, with 7 haplotypes being unique and 2 haplotypes being shared among the 5 populations. The phylogenetic analysis using Neighbor-joining (NJ) and maximum-parsimony (MP) methods supported the monophyletic status between T. tambroides and T. douronensis, thus suggesting their status as different species. The clustering of all T. tambroides samples into a single clade suggested that their genetic identity belongs to a single species. The sharing of haplotype HKE4 between Batang Ai of Sarawak (n = 4) and Perak of Peninsular Malaysia (n = 3) reflects the historical connection of drainages between the regions possibly during Pleistocene glaciation periods. Limited variations were found among all peninsular T. tambroides populations. The low level of mitochondrial (mt)DNA differences currently found among T. tambroides populations is probably due to the high proportion of the HKE1 haplotype being found in all the populations (0.736 - 1.000), or the small number of samples used in the present study. Overall, the present study was able to shed light on the phylogenetic relationships and genetic structure of T. tambroides in Malaysia.
The need to detect genetic variation has fueled the development of novel marker systems in fisher... more The need to detect genetic variation has fueled the development of novel marker systems in fisheries biology. In this study, a simple, fast and cost effective method was used to differentiate between species of freshwater fishes focusing on Malaysian freshwater fishes by employing Restriction Fragment Length Polymorphisms (RFLPs) analysis of a 470-bp cytochrome b mtDNA segment. RFLP analysis using six restriction enzymes (AluI, BamHI, BsuRI, Csp61, HpaII and SalI) found variations in the digestion profile among most of the fish samples analyzed. Diagnostic digestion profiles were observed among the Hampala fishes, especially between H. macrolepidota and the other Hampala species/forms (using BsuRI and Csp61). Diagnostic digestion profiles were also detected between H. bimaculata Type A and Type B (using AluI, BamHI, BsuRI and SalI), supporting their status as distinct species. Additionally, unique digestion profiles were observed in other species such as Leptobarbus hosii (Csp61), Osteocheilus hasseltii (Csp61), Osteocheilus sp. (Csp61), Puntioplites bulu (Csp61), Puntius bramoides (AluI), P. sealei (AluI) and Helostoma temmincki (AluI and Csp61), which can be used as genetic markers for discriminating these species. Overall, the RFLP analysis of the cytochrome b mtDNA segment has proven to be a considerably effective, fast and non-expensive technique to discriminate among several freshwater fish species in Malaysia.
Surveys on the distribution of fish fauna in Serting River and Jempol River, Negeri Sembilan were... more Surveys on the distribution of fish fauna in Serting River and Jempol River, Negeri Sembilan were conducted from 24-30thMarch 2002. Collection was made at eight stations where river conditions varied from highly disturbed to undisturbed. A total of 41 fish species belonging to 16 families was identified. Analyses based on the number of individuals caught showed that 79.7% of total catch was represented by the Cyprinid. Present study showed that both rivers were inhabited by several introduced species such as Clarias gariepinus, Colossoma sp., Hypostomus sp. and Oreochromis sp. Species diversity, density and richness were also calculated for all the stations.
Zoological Science, Jan 1, 2006
This study examined 396 base pairs of the mitochondrial DNA cytochrome b gene from 110 individual... more This study examined 396 base pairs of the mitochondrial DNA cytochrome b gene from 110 individuals belonging to the genus Hampala, a group of primary freshwater cyprinids that inhabit Southeast Asia. The samples were taken from various locations throughout Sarawak, Sabah and peninsular Malaysia. The nucleotide sequences were subjected to phylogenetic analyses by using the neighbor-joining, maximum parsimony and maximum likelihood methods. All three methods revealed the reciprocally monophyletic relationship of Hampala macrolepidota from the other Hampala forms, thus strongly supporting its status as a distinct species. Phylogenetic analysis also discovered the existence of two H. bimaculata lineages endemic to Borneo: (1) a newly identified species from the southern and central part of Sarawak assigned as H. bimaculata Type A and (2) the previously described H. bimaculata from northern Sarawak and the west coast of Sabah assigned as H. bimaculata Type B. However, the status of H. sabana and an intermediate form were not elucidated. The results suggest that the intermediate form from the Tawau population is actually a subpopulation of H. sabana while the highly divergent intermediate form from Kalabakan could represent a cryptic species. The sharing of H. macrolepidota haplotypes in the southern peninsular Malaysia and southern and central Sarawak samples (Hm1 and Hm2) reflected the recent disconnection of the two regions, during the last Pleistocene. Overall, the partial sequence of the cytochrome b gene was useful for resolving the phylogenetic relationships among Hampala fishes in Malaysia.
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Papers by Rovie-Ryan Jeffrine J
role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR)
markers have successfully been tested for investigating the genetic diversity of malaria
vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic
variation of Plasmodium species, as well. To illustrate the genetic diversity of two
infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium
cynomolgi, infected and uninfected monkey blood samples were separately collected on
filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic
ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis
of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of
three clusters. However, the most significant result of the cluster analysis was revealing
the high efficiency of ISSR markers in the discrimination of the two Plasmodium species
from each other. The cluster analysis showed a wide range of genetic diversity among both
Plasmodium and the long-tailed Macaque accessions. The principal component analysis
(PCA) also confirmed the cluster analysis results.
constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. Conclusions: This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases.
role in controlling and preventing this lethal infection. Inter simple sequence repeat (ISSR)
markers have successfully been tested for investigating the genetic diversity of malaria
vectors. It is hypothesized that ISSRs could lead to fruitful results in studying the genetic
variation of Plasmodium species, as well. To illustrate the genetic diversity of two
infectious Plasmodium species, including Plasmodium knowlesi and Plasmodium
cynomolgi, infected and uninfected monkey blood samples were separately collected on
filter papers (FTA cards), and used for DNA extraction. A total of 103 and 95 polymorphic
ISSR loci were detected in infected and uninfected samples, respectively. Cluster analysis
of the Plasmodium and Macaca fascicularis accessions both resulted in the generation of
three clusters. However, the most significant result of the cluster analysis was revealing
the high efficiency of ISSR markers in the discrimination of the two Plasmodium species
from each other. The cluster analysis showed a wide range of genetic diversity among both
Plasmodium and the long-tailed Macaque accessions. The principal component analysis
(PCA) also confirmed the cluster analysis results.
constructed phylogenetic trees confirmed the blood meal samples were indeed from the rhino. Conclusions: This method could be used in the field application to noninvasively collect genetic samples. Collection of tabanids and other haematophagous arthropods (e.g. mosquitoes and ticks) and other blood-sucking parasites (e.g. leeches and worms) could also provide information on vector-borne diseases.