Ian Kendrich C. Fontanilla
Doctor of Philosophy in Genetics, University of Nottingham, United Kingdom, 2010
Field of Specialization
Article title: Analysis of Environmental DNA and Edaphic Factors for the Detection of the Snail Intermediate Host Oncomelania hupensis quadrasi
Authors: Fritz Ivy Calderon Calata, Camille Z. Caranguian, Jillian Ela Mamaril Mendoza, Raffy Jay Fornillos, et al.
Publication title: Pathogens 8(4): 160, September 2019
Background: The perpetuation of schistosomiasis japonica in the Philippines depends to a major extent on the persistence of its intermediate host Oncomelania hupensis quadrasi, an amphibious snail. While the malacological survey remains the method of choice in determining the contamination of the environment as evidenced by snails infected with schistosome larval stages, an emerging technology known as environmental DNA (eDNA) detection provides an alternative method. Previous reports showed that O. hupensis quadrasi eDNA could be detected in water, but no reports have been made on its detection in soil. Methods: This study, thus focused on the detection of O. hupensis quadrasi eDNA from soil samples collected from two selected schistosomiasis-endemic barangays in Gonzaga, Cagayan Valley using conventional and TaqMan-quantitative (qPCR) PCRs. Results: The results show that qPCR could better detect O. hupensis quadrasi eDNA in soil than the conventional method. In determining the possible distribution range of the snail, basic edaphic factors were measured and correlated with the presence of eDNA. The eDNA detection probability increases as the pH, phosphorous, zinc, copper, and potassium content increases, possibly indicating the conditions in the environment that favor the presence of the snails. A map was generated to show the probable extent of the distribution of the snails away from the body of the freshwater. Conclusion: The information generated from this study could be used to determine snail habitats that could be possible hotspots of transmission and should, therefore, be targeted for snail control or be fenced off from human and animal contact or from the contamination of feces by being a dumping site for domestic wastes.
Article title: Complete Mitochondrial Genome and Novel Gene Organization of Ryssota otaheitana (Pulmonata: Chronidae), and its Implications on the Stylommatophora Phylogeny
Authors: Amor Li Damatac, Ian Kendrich Carandang Fontanilla
Publication title: Philippine Journal of Science 148(S1): 167-180, August 2019
Whole mitochondrial genomes (mitogenomes) have been increasingly used as markers for phylogenetic inferences. In the Philippines, a marine snail from the Conidae family has been the only species to date whose mitogenome has been fully sequenced, despite the country’s rich malacofaunal diversity particularly in the terrestrial environment. In this study, we sequenced the complete mitogenome of the land snail Ryssota otaheitana (Chronidae), an endemic Philippine pulmonate species. The mitogenome is 13,888 bp in length and encodes the typical 37 genes – including 13 protein-coding, 22 tRNA, and 2 rRNA genes. Short intergenic spacers were found – including a reduced, 42-bp putative control region. Although the gene content is conserved, R. otaheitana showed a novel mitogenome organization involving the translocation of tRNASerine and NADH dehydrogenase subunit 4 gene segment. Combined with available stylommatophoran mitogenomes, different datasets from concatenated sequences of protein-coding and rRNA genes were used for phylogenetic reconstructions. Bayesian Inference (BI) and Maximum Likelihood (ML) trees congruently supported several monophyletic clades within the Stylommatophora such as the Helicoidea, Urocoptoidea, Orthurethra, and Limacoidea sensu lato (syn. ‘limacoid clade’). R. otaheitana is grouped with Deroceras reticulatum in the lower Stylommatophora and forms the monophyletic Limacoidea sensu lato. Both sequence-based phylogeny and gene order comparisons have led us to a hypothesis that Limacoidea sensu lato is at the base of the ‘non-achatinoid’ clade while supporting the division of ‘achatinoid and ‘non-achatinoid’ groups in the Stylommatophora. This study reports the first complete mitogenome from the Chronidae family, which can be used further for the molecular phylogeny of Philippine snails and gastropods at large.
Article title: Forensic entomology in the Philippines: Establishing Baseline Data on the Forensically Important Blow Fly Species Chrysomya megacephala (Fabricius, 1794)
Authors: Ronniel Pedales, Ian Kendrich Carandang Fontanilla
Publication title: Philippine Journal of Science 147(1): 17-25, March 2018
The Philippines is yet to adapt and implement guidelines and protocols in forensic entomology, particularly establishing local databases. Considering the efforts made by neighboring Southeast Asian countries in the field, the nation has been left behind in insect evidence-based investigations. Of utmost importance to forensic entomology are blow flies (Diptera: Calliphoridae), which are primary colonizers of carrion. Through knowledge of their distribution, identity, and growth rates, investigators are able to provide a post-mortem interval that is most accurate after the onset of putrefaction. The Philippines has a total of 83 blow fly species recorded, including the cosmopolitan species Chrysomya megacephala. This paper aims to establish a baseline reference in Philippine forensic entomology by mapping the distribution, providing DNA barcodes, and estimating larval growth rates from oviposition to pupariation of C. megacephala. Distribution data were mapped in QGIS using localities from fieldwork data in this study and those in the Key to the Philippine Calliphoridae by Kurahashi and Magpayo. DNA barcodes of specimens from Isabela, Quezon City, and Marinduque in the Philippines matched with C. megacephala from the database in GenBank and revealed a possible SNP in the fragment amplified. C. megacephala was reared from oviposition in a simple incubation set-up to estimate the duration of development to pupariation, which ranged 100-113 hours. This is the first study on the distribution, molecular identification, and development of C. megacephala in the Philippines. Further work is needed to distinguish among populations of the species and to construct more precise growth curves.
Article title: Genetic Comparison of Oncomelania hupensis quadrasi Genetic Comparison of Oncomelania hupensis quad rasi (Möllendorf, 1895) (Gastropoda: Pomatiopsidae), the Intermediate Host of Schistosoma japonicum in the Philippines, Based on 16S Ribosomal RNA Sequence Online
Authors: James Christopher Chua, Ian Kim Basas Tabios, Pebbles Grayle Panado Tamayo, Lydia Leonardo, et al
Publication title: PLoS One 14(11): e0224617, 2019
Schistosomiasis japonica is a water-borne trematode infection transmitted by different subspecies of Oncomelania hupensis. As parasites may either co-evolve or locally adapt with their hosts, snail diversity, as revealed by morphometric and genetic studies, may reflect parasite diversity and elucidate snail susceptibility and transmission patterns. This study aimed to compare isolates of O. h. quadrasi based on a 342-bp fragment of the 16S ribosomal RNA gene. O. h. quadrasi isolates were collected from nine provinces known to have S. japonicum in the Philippines, namely Cagayan Valley, Bohol, Negros Occidental, Leyte, Davao, Davao del Sur, Mindoro Oriental, Northern Samar, and Sorsogon. O. h. hupensis and O. h. nosophora isolates were also collected from China and Japan, respectively. The 16S ribosomal RNA gene of each specimen was amplified and sequenced. Phylogenetic and network analyses based on the 221 16S rRNA gene sequences revealed that O. h. quadrasi clustered as a distinct clade from the two other subspecies. Of the four identified haplotypes for O. h. quadrasi, two haplotypes were from Negros Oriental (Ohq2 and Ohq3), and one haplotype was from Bohol (Ohq4). The isolates from the remaining seven provinces shared a common haplotype (Ohq1). The current study was able to show the relationship among O. hupensis subspecies and demonstrate the limited ability of mitochondrial 16S ribosomal molecular marker in differentiating O. h. quadrasi geographic strains in the Philippines.
Article title: Geographic strain differentiation of Schistosoma japonicum in the Philippines using microsatellite markers
Authors: Kharleezelle J. Moendeg, Jose Ma. M. Angeles, Ryo Nakao, Lydia Leonardo, et al.
Publication title: PLoS Neglected Tropical Diseases 11(7), July 2017
Background: Microsatellites have been found to be useful in determining genetic diversities of various medically-important parasites which can be used as basis for an effective disease management and control program. In Asia and Africa, the identification of different geographical strains of Schistosoma japonicum, S. haematobium and S. mansoni as determined through microsatellites could pave the way for a better understanding of the transmission epidemiology of the parasite. Thus, the present study aims to apply microsatellite markers in analyzing the populations of S. japonicum from different endemic areas in the Philippines for possible strain differentiation. Methodology/ principal findings: Experimental mice were infected using the cercariae of S. japonicum collected from infected Oncomelania hupensis quadrasi snails in seven endemic municipalities. Adult worms were harvested from infected mice after 45 days of infection and their DNA analyzed against ten previously characterized microsatellite loci. High genetic diversity was observed in areas with high endemicity. The degree of genetic differentiation of the parasite population between endemic areas varies. Geographical separation was considered as one of the factors accounting for the observed difference between populations. Two subgroups have been observed in one of the study sites, suggesting that co-infection with several genotypes of the parasite might be present in the population. Clustering analysis showed no particular spatial structuring between parasite populations from different endemic areas. This result could possibly suggest varying degrees of effects of the ongoing control programs and the existing gene flow in the populations, which might be attributed to migration and active movement of infected hosts from one endemic area to another. Conclusions/ significance: Based on the results of the study, it is reasonable to conclude that genetic diversity could be one possible criterion to assess the infection status in highly endemic areas. Genetic surveillance using microsatellites is therefore important to predict the ongoing gene flow and degree of genetic diversity, which indirectly reflects the success of the control program in schistosomiasis-endemic areas.
Article title: A review of the current taxonomic status of foliose Bangiales (Rhodophyta) in the Philippines
Authors: Richard V. Dumilag, Zae-Zae Aguinaldo, Cynthia Mintu, Myrna Quinto, et al.
Publication title: Phytotaxa 312(1): 47-49, July 2017
Causes of taxonomic confusion are lamentably well known in foliose Bangiales. A magnitude of these uncertainties stems from the paucity of available taxonomic traits in morphologically homoplastic species. At present, the taxonomic identity and systematics of many of the Philippine foliose Bangiales are in a state of flux. A critical examination of published literature on Philippine records of 10 species of foliose Bangiales has rendered the need for re-confirmation of the presence of Porphyra atropurpurea, Porphyra marcosii, Pyropia denticulata, and Pyropia suborbiculata while records of Porphyra umbilicalis, Pyropia vietnamensis, Wildemania variegata, and the invalid name Porphyra crispata have been omitted from the list. Currently, there are only two confirmed species of foliose Bangiales in the Philippines, which are Pyropia acanthophora and Pyropia tanegashimensis. Thus, this review exhorts a re-examination of collected Philippine foliose Bangiales materials using both morphological and molecular analysis.
Full text available upon request to the author
Article title: Molecular phylogeny of the Achatinoidea (Mollusca: Gastropoda)
Authors: Ian Kendrich C. Fontanilla, Fred Naggs, Christopher M. Wade
Publication title: Molecular Phylogenetics and Evolution 114, June 2017
This study presents a multi-gene phylogenetic analysis of the Achatinoidea and provides an initial basis for a taxonomic revaluation of family level groups within the superfamily. A total of 5028 nucleotides from the nuclear rRNA, actin and histone 3 genes and the 1st and 2nd codon positions of the mitochondrial cytochrome c oxidase subunit I gene were sequenced from 24 species, representing six currently recognised families. Results from maximum likelihood, neighbour joining, maximum parsimony and Bayesian inference trees revealed that, of currently recognised families, only the Achatinidae are monophyletic. For the Ferussaciidae, Ferussacia folliculus fell separately to Cecilioides gokweanus and formed a sister taxon to the rest of the Achatinoidea. For the Coeliaxidae, Coeliaxis blandii and Pyrgina umbilicata did not group together. The Subulinidae was not resolved, with some subulinids clustering with the Coeliaxidae and Thyrophorellidae. Three subfamilies currently included within the Subulinidae based on current taxonomy likewise did not form monophyletic groups.
Article title: DNA barcoding, population genetics, and phylogenetics of the illegally hunted Philippine Duck Anas luzonica (Aves: Anseriformes: Anatidae)
Authors: Arde Mingoa Licuanan, Mariano Roy Duya, Perry S. Ong, Ian Kendrich Carandang Fontanilla
Publication title: Journal of Threatened Taxa 9(5): 10141, May 2017
DNA barcoding is extensively used as a species identification and delineation tool. The aim of this study was to generate a barcode profile for mitochondrial cytochrome c oxidase subunit 1 (COI) in the Philippine Duck Anas luzonica, a dabbling duck species endemic to the Philippines that is classified as ‘Vulnerable’ by the International Union for Conservation of Nature (BirdLife International 2016). COI barcodes were successfully obtained using muscle tissue samples from 46 A. luzonica individuals confiscated from illegal hunters in Pantabangan, Nueva Ecija. Analysis of TrN+Γ+I distances among the Anas luzonica COI sequences and those of 25 other Anas species revealed that COI barcodes cannot generally delineate hybridizing species. While Anas luzonica was differentiated from other species it is known to hybridize with and formed a monophyletic group in the neighbor-joining tree generated, sampling from areas of sympatry is needed since individuals were obtained from only one sampling site. The population structure of the Anas luzonica population was also examined using mitochondrial DNA control region and COI sequences. The population had high haplotype diversity and low nucleotide diversity, an indication that a bottleneck event had occurred, which is likely due to extreme hunting pressures and habitat destruction. The population under study exhibited high genetic diversity. Given that the samples for this study came from a single locality, sampling from other localities is required to determine whether other populations are facing the risk of reduced fitness (inbreeding depression).
Article title: First record of the Charru mussel Mytella charruana d'Orbignyi, 1846 (Bivalvia: Mytilidae) from Manila Bay, Luzon, Philippines
Authors: Benjamin Vallejo, Jennifer Conejar-Espedido, Leanna Manubag, Kevin Carlo, et al.
Publication title: BioInvasions Records 6(1), January 2017
This study reports the presence of the Charru mussel Mytella charruana d'Orbignyi, 1846 (Bivalvia: Mytilidae) in Manila South Harbor, Manila Bay, Luzon Island, Philippines. In 2014, mussels previously identified as Mytilus spp. were reported in Manila Bay. The species was detected as part of an ecological dynamics study of previously-recorded marine non-indigenous mollusc species. DNA barcoding results suggest that the previously identified Mytilus are in fact Mytella charruana with an average identity match of 94%. The trends in abundance of Mytella during the 2014–2015 sampling season are described and the potential of this new species to become invasive and competitive with native Perna viridis (Linnaeus, 1758).
Article title: Determining species identity from confiscated pangolin remains using DNA barcoding
Authors: Adrian U. Luczon, Perry S. Ong, Jonas Quilang, Ian Kendrich Carandang Fontanilla
Publication title: Mitochondrial DNA Part B 1(1): 763 -766, October 2016
Illegal wildlife trade is one of the key threats to biodiversity. A requisite in combating illegal wildlife trade is through effective and efficient identification of confiscated wildlife or wildlife remains. This can be done through DNA barcoding. In this study, DNA barcoding was employed on several cases of poaching in the Philippines involving 85 unidentified pangolin remains. Of these, 73 specimens confiscated from Palawan were identified as the Palawan endemic Manis culionensis, but no deep divergences were observed, suggesting that the samples originated from a single locality. The other 12 individuals, which were part of a large haul of pangolin carcasses recovered from a foreign fishing vessel that ran aground in Tubattaha Reefs, Philippines, were identified as the Malayan Pangolin, M. javanica. They split into two groups with 3.3% mean genetic distance, suggesting at least two geographic origins.
Article title: Review Schistosomiasis In The Philippines: Challenges And Some Successes In Control
Authors: Lydia Leonardo, Yuichi Chigusa, Mihoko Kikuchi, Naoko Kato-Hayashi, et al.
Publication title: The Southeast Asian Journal of Tropical Medicine and Public Health 47(4), August 2016
Schistosomiasis is a snail-borne neglected tropical disease affecting 78 countries and territories in Africa, Asia, South America and the Middle East.Three species are highly pathogenic to man namely Schistosoma japonicum, S. mansoni and S. haematobium. In the Philippines, the endemic species is S. japonicum to which 2.5 million Filipinos are directly exposed. This paper describes schistoso-miasis in the Philippines, the status of the disease, the efforts in controlling it, the numerous problems in the implementation of the control program and good practices developed in endemic areas that have contributed to even limited success and possible prospects in control of the disease. It traces the history of the control program from the time that the disease was discovered in 1906 and cites various administrative orders that provided for the implementation of the different components of the program. Much of the information contained in this paper were collated from the program implementation review of the control program in 2012, consultative meetings conducted in 2013 with health officials involved in the program, reports delivered in the 15 th meeting of the RNAS+ in July 2015, personal communications with program implementers in endemic areas visited in researches of the principal author, and her research team. The principal author was involved in all these activities and wrote the final reports.
Article title: Vectors and Spatial Patterns of Angiostrongylus cantonensis in Selected Rice-Farming Villages of Muñoz, Nueva Ecija, Philippines
Authors: Angelica Tujan, Ian Kendrich Carandang Fontanilla, Vachel Gay Paller
Publication title: Journal of Parasitology Research 2016(2): 1-7, May 2016
In the Philippines, rats and snails abound in agricultural areas as pests and source of food for some of the local people which poses risks of parasite transmission to humans such as Angiostrongylus cantonensis . This study was conducted to determine the extent of A. cantonensis infection among rats and snails collected from rice-farming villages of Muñoz, Nueva Ecija. A total of 209 rats, 781 freshwater snails, and 120 terrestrial snails were collected for the study. Heart and lungs of rats and snail tissues were examined and subjected to artificial digestion for parasite collection. Adult worms from rats were identified using SSU rDNA gene. Seven nematode sequences obtained matched A. cantonensis . Results revealed that 31% of the rats examined were positive with A. cantonensis . Rattus norvegicus and R. tanezumi showed prevalence of 46% and 29%, respectively. Furthermore, only Pomacea canaliculata (2%) and Melanoides maculata (1%) were found to be positive for A. cantonensis among the snails collected. Analysis of host distribution showed overlapping habitats of rats and snails as well as residential and agricultural areas indicating risks to public health. This study presents a possible route of human infection for A. cantonensis through handling and consumption of P. canaliculata and M. maculata or crops contaminated by these snails.
Article title: Characterization of an isolate of Heterorhabditis bacteriophora (Nematoda: Heterorhabditidae) from the Northern Territory, Australia, using morphology and molecular data
Authors: John Henry Hernandez Sagun, Kerrie A. Davis, Ian Kendrich Carandang Fontanilla, Merab Antone Chan
Publication title: Zootaxa 4040(1): 17, November 2015
An entomopathogenic nematode, Heterorhabditis H39, was found in Darwin, Australia. Based on morphological and mor-phometric similarities, and molecular characterisation, it is an isolate of Heterorhabditis bacteriophora. Males, hermaphrodites, females and juveniles showed important similarities on most characters that define H. bacteriophora. The morphometrics of the infective juvenile of Heterorhabditis H39 are similar to those of H. bacteriophora, including average body length (562 (537-587) vs 570 (520-600) μm), maximum body width (21 (19-22) vs 24 (21-31) μm), distance from the anterior end to the EP (96 (87-104) vs 104 (94-109) μm) and tail length (101 (94-111) vs 91 (83-99) μm). The morphology of the spicules and gubernaculum of male Heterorhabditis H39 are indistinguishable from those of H. bacteriophora. The biology and life cycle of Heterorhabditis H39 are similar to those of other Heterorhabditis species. The Neighbour-Joining Tree based on 475 nucleotides of the SSU rRNA gene showed that Heterorhabditis H39 formed a monophyletic group with other H. bacteriophora isolates with a bootstrap value of 100. Thus, phylogenetic study of SSU sequence data provided strong evidence that Heterorhabditis H39 is an isolate of H. bacteriophora. This is the first record of H. bacteriophora in northern Australia.
Article title: A new Helicostyla species (Bradybaenidae: Helicostylinae) from Patnanungan Island, Philippines
Authors: Emmanuel Ryan C. de Chavez, Ian Kendrich Carandang Fontanilla, Gizelle Batomalaque, Satoshi Chiba, et al.
Publication title: Asia Life Sciences 24(1): 37-49, January 2015
A new species of land snail, Helicostyla amagaensis de Chavez, belonging to Subfamily Helicostylinae, Family Bradybaenidae is described from a native dipterocarp forest in Patnanungan Island, Polillo Group of Islands, Philippines. This new species differs from other congeners by its ovate-globose, cream white shell with single chestnut brown band. Aperture is ovate and moderately oblique with reddish-brown streak around the aperture outer lip. Penis is long with inner oblique striations terminating towards a leaf-like stimulator. Vas deferens is short and flagellum is absent. DNA barcoding technique using Cytochrome c oxidase I subunit (COI) revealed H. amagaensis has closest sequence affinity with Helicostyla woodiana. Neighbor joining and maximum parsimony trees showed 100% bootstrap support for the inclusion of this new species as a member of the genus Helicostyla. This is the latest Helicostyla discovered in the Philippines and the third helicostyline snail that is endemic to the Polillo Group of Islands.
Article title: An Updated Survey and Biodiversity Assessment of the Terrestrial Snail (Mollusca: Gastropoda) Species in Marinduque, Philippines
Authors: Benjamin O. Sosa III, Gizelle A. Batomalaque, Ian Kendrich C. Fontanilla
Publication title: Philippine Journal of Science 143(2): 199-210, December 2014
Marinduque is an island province of volcanic origin and is found in the southern portion of the Luzon Group of Islands. The island has an uneven topography but has experienced drastic deforestation in recent times. Records on the terrestrial snail species diversity in the Philippines in general and Marinduque in particular are sparse in the zoological literature. Previous literature noted only 13 species in Marinduque, which could be a gross underestimation of the terrestrial malacofaunal diversity of the island because the area was not systematically surveyed. This study aimed to assess the malacofaunal biodiversity of Marinduque and prepare a comprehensive list of snail taxa via opportunistic sampling. Sampling was conducted in 12 pre-determined areas of the island, with emphasis on minimally disturbed areas. This study reported ten (10) new records of stylommatophoran species and six (6) new records of terrestrial prosobranch species in Marinduque, which brings a total of 24 terrestrial snail species known to date (or 26 if two previously recorded species that were not encountered in this study are included).
Article title: Restricted Genetic Variation in Populations of Achatina (Lissachatina) fulica outside of East Africa and the Indian Ocean Islands Points to the Indian Ocean Islands as the Earliest Known Common Source
Authors: Ian Kendrich Fontanilla, Ina Mikaella P. Sta Maria, James Rainier M. Garcia, Hermant Ghate, et al.
Publication title: PLoS ONE 9(9), September 2014
The Giant African Land Snail, Achatina ( = Lissachatina) fulica Bowdich, 1822, is a tropical crop pest species with a widespread distribution across East Africa, the Indian subcontinent, Southeast Asia, the Pacific, the Caribbean, and North and South America. Its current distribution is attributed primarily to the introduction of the snail to new areas by Man within the last 200 years. This study determined the extent of genetic diversity in global A. fulica populations using the mitochondrial 16S ribosomal RNA gene. A total of 560 individuals were evaluated from 39 global populations obtained from 26 territories. Results reveal 18 distinct A. fulica haplotypes; 14 are found in East Africa and the Indian Ocean islands, but only two haplotypes from the Indian Ocean islands emerged from this region, the C haplotype, now distributed across the tropics, and the D haplotype in Ecuador and Bolivia. Haplotype E from the Philippines, F from New Caledonia and Barbados, O from India and Q from Ecuador are variants of the emergent C haplotype. For the non-native populations, the lack of genetic variation points to founder effects due to the lack of multiple introductions from the native range. Our current data could only point with certainty to the Indian Ocean islands as the earliest known common source of A. fulica across the globe, which necessitates further sampling in East Africa to determine the source populations of the emergent haplotypes.
Article title: Genetic diversity of the Critically Endangered Philippine Eagle Pithecophaga jefferyi (Aves: Accipitridae) and notes on its conservation
Authors: Adrian U. Luczon, Ian Kendrich C. Fontanilla, Perry S. Ong, Basiao Zu, et al.
Publication title: Journal of Threatened Taxa 6: 6335-6344, September 2014
The Philippine Eagle Pithecophaga jefferyi is a diurnal raptor endemic to the Philippines. Its distribution is restricted to remaining forests on the islands of Luzon, Samar, Leyte and Mindanao. The Philippine Eagle is classified as a Critically Endangered species under the IUCN Red List, with a high end estimated population of only 500 breeding pairs in the wild. Population decline has been attributed to continuing deforestation, particularly since the mid-1900s, and hunting. This study aimed to identify the effects of population decline on the genetic structure of the present population of the Philippine Eagle by sequencing 1132bp of the mitochondrial control region from 22 individuals. Control region haplotype diversity (h = 0.8960±0.05590) and nucleotide diversity (π = 0.006194±0.003372) are comparable with other accipitrid species. Maximum likelihood trees and network analysis show that the Luzon and Samar individuals come from different lineages, but both shared a common ancestral population with the Mindanao population. The genetic diversity, multimodal mismatch distribution for the control region and high frequency of lower class modes all indicate a recent bottleneck for the Philippine Eagle population. Possible strategies for conservation are discussed.
Article title: Identification of Angiostrongylus cantonensis and other nematodes using the SSU rDNA in Achatina fulica populations of Metro Manila
Authors: M. A. Constantino Santos, Z. U. Basiao, Christopher M. Wade, Brian S. Santos, et al.
Publication title: Tropical Biomedicine 31(2): 327-35, June 2014
Angiostrongylus cantonensis is a parasitic nematode that causes eosinophilic meningitis in humans. Accidental infection occurs by consumption of contaminated intermediates, such as the giant African land snail, Achatina fulica. This study surveyed the presence of A. cantonensis juveniles in A. fulica populations from 12 sites in Metropolitan Manila, Philippines using the SSU rDNA. Fourteen distinct sequences from 226 nematodes were obtained; of these, two matched A. cantonensis and Ancylostoma caninum, respectively, with 100% identity. Exact identities of the remaining twelve sequences could not be determined due to low percent similarities. Of the sequenced nematodes, A. cantonensis occurred with the highest frequency (139 out of 226). Most of these (131 out of 139) were collected in just one area in Quezon City. Nematode infection of A. fulica in this area and two others from Makati and another area in Quezon City, respectively, were highest, combining for 95% of the total infection. Ancylostoma caninum, on the other hand, was detected in four different sites. A. caninum is a canine parasite, and this is the first report of the nematode in A. fulica. These results cause public health concerns as both A. cantonensis and A. caninum are zoonotic to humans.
Article title: Biodistribution of the Informal Group Basommatophora in the Philippines
Authors: Patrick Noel, Y. Young, Ian Kendrich C. Fontanilla
Publication title: Science Diliman 26(1): 53-76, January-June 2014
Basommatophora is an informal group within the molluscan subclass Pulmonata comprising of air-breathing freshwater snails that are typically characterized by eyespots located at the base of two noncontractile tentacles and two external genital orifices. They also have varied shell structures and habitats, not only within the group but also within families. Families of the Basommatophora are highly ubiquitous and may play a role in the life cycles of various parasites of humans and animals. Basommatophora has a worldwide geographical distribution across freshwater, terrestrial and marine habitats. However, little is known on their distribution in the Philippines. This report focuses on describing the biogeographical distribution of the basommatophorans in the Philippines through data gathered from museum collections, foreign databases accessed online, and identification of species found in various literatures. A qualitative description of the distribution of each Basommatophora family in the Philippines is given by distribution maps, indicating locations where specimens were collected and/or identified. A total of 336 counts of basommatophorans from 22 genera were encountered from available literature, museums and public databases. The majority of the occurrences are from the genera Siphonaria. The data and maps generated describe most of the distribution to be in Luzon, with Visayas and Mindanao having close counts with each other. The Philippines has the third most occurrences and genera of basommatophorans of all tropical countries in the world. However, the true diversity of the group could be higher if a more systematic sampling of the archipelago is conducted. Keywords: Basommatophora, Philippines, biogeographical distribution
Article title: DNA barcoding using cytochrome oxidase I (COI) of pulmonate gastropods from Batan Island, Batanes, Philippines
Authors: Gizelle Batomalaque, Paul Ryan Littaua Sales, Ian Kendrich C. Fontanilla
Publication title: Asia Life Sciences 22(2): 341-357, July 2013
DNA barcoding has emerged as a powerful tool for species identification, with the cytochrome c oxidase subunit I gene (COI) gene as the marker of choice for animals. In the Philippines, barcoding has focused primarily on fish, birds and plants, with less emphasis on snails. This study reports, for the first time, the COI sequences of pulmonates collected from Batan Is., Batanes. Five species belonging to five different families were sequenced for the 655 bp partial coding region of the COI gene. These are Eulota mighelsiana (Family Bradybaenidae), Ryssota sagittifera batanica (Family Helicarionidae), Satsuma batanica (Family Camaenidae), Trochornorpha troilus (Family Trochomorphidae) and Sarasinula plebeia (Family Veronicellidae). All available COI sequences of species under the identified families were obtained from GenBank. A total of 377 sequences, with 589 bp length, were analyzed from 136 species. Of the five species from Batan Is., only S. batanica had a conspecific match (99.7% similarity) from GenBank. The other four are novel. Base frequencies and GC contents are relatively similar for all families. An apparent bias against C was observed and most variations occurred at the 3rd codon position.
Full text available upon request to the author
Article title: DNA Barcoding of Birds in the University of the Philippines Diliman Campus, with Emphasis on Striated Grassbirds Megalurus palustris
Authors: Adrian U. Luczon, Andrew F. Torres, Jonas Quilang, Perry S. Ong, et al.
Publication title: Philippine Journal of Science 142(1): 1-11, June 2013
DNA barcoding is increasingly being used by researchers across the globe to aid in the identification of species. Using this taxonomic tool on bird species in an urban green space within Manila, i.e. the University of the Philippines Diliman campus, Luzon, Philippines, DNA barcodes of eleven species were generated. Different haplotypes for some of the species were observed. Using BLAST, the cytochrome oxidase subunit 1 (COI) sequence of every species from this study was correctly matched with the corresponding species having a COI record in Genbank, with the exception of the Striated Grassbird Megalurus palustris, which is a new COI record. The three distinct haplotypes for M. palustris were then compared with COI sequences from other members of the sylviid " Old World Warblers " to determine the effectiveness of the DNA barcode in discriminating it with other species. Results show that COI was successful in placing M. palustris as a distinct taxon.
Article title: First report of Angiostrongylus cantonensis in the Giant African Land Snail Achatina fulica in French Polynesia detected using the SSU rRNA gene
Authors: Ian Kendrich C. Fontanilla and Christopher M. Wade
Publication title: Tropical Biomedicine 29(4): 642-5, December 2012
The 5' end of the small subunit ribosomal RNA gene was used to determine whether 3rd larval stage Angiostrongylus cantonensis are present in populations of the giant African land snail Achatina fulica from French Polynesia. Two populations, one from Moaroa Valley, Tahiti (n=5) and the other from Haapiti Valley, Moorea (n=10), were examined. All snails from Tahiti were infected with nematodes, with parasite load ranging from 12 to 28. A total of 92 nematodes were found, of which 91 were positively identified as A. cantonensis. No nematodes were found in the snails from Moorea. We report for the first time the presence of A. cantonensis in A. fulica snails from French Polynesia, indicating a viable route of human infection of A. cantonensis in the region through the handling of A. fulica or consumption of the snail or contaminated food crops associated with the snail.
Article title: Distribution of MN blood group types in local populations in Philippines
Authors: Anna Elvira S. Arcellana, Ruth Marian Guzman, Ian Kendrich C. Fontanilla
Publication title: Journal of Genetics 90(3), December 2011
Article title: DNA Barcoding of the Philippine Endemic Freshwater Sardine Sardinella tawilis (Clupeiformes: Clupeidae) and Its Marine Relatives
Authors: Jonas Quilang, Brian S. Santos, Perry S. Ong, Zubaida U. Basiao, et al.
Publication title: Philippine Agricultural Scientist 94(3), October 2011
Sardinella tawilis (Herre, 1927), the only freshwater sardine in the world, is endemic to Taal Lake, Philippines. It is a major fishery resource in the area. In this study, DNA barcoding using cytochrome c oxidase subunit I (COI) gene was performed on Sardinella tawilis and its marine relatives S. fimbriata, S. jussieu, S. lemuru and Nematalosa nasus. Additional sequences from S. albella, S. atricauda, S. gibbosa S. jussieu, S. lemuru, S. longiceps and S. melanura were obtained from GenBank. A total of 54 sequences were analyzed. The Kimura 2-parameter (K2P) distance model was used to compute the divergences of sequences within and between species and to generate a Neighbour-joining (NJ) tree. The mean intraspecific genetic distance was 0.3%, whereas the mean interspecific genetic distance was 15.2%. The genetic distance of S. tawilis from other Sardinella species ranged from 16.4% to 19.3%. S. tawilis also formed a distinct cluster in the NJ tree that is well-separated from the other species. These findings contrast with the suggestion in previous studies that S. tawilis and S. albella are ecomorphs of the same species and are not truly differentiated species based on mitochondrial control region sequence and multivariate analysis of morphological characters. This study is the first to report the occurrence of S. jussieu in the Philippines. Out of the five S. jussieu COI sequences generated in this study, two clustered with S. fimbriata, while the other three clustered with S. jussieu sequences from GenBank. Although S. fimbriata and S. jussieu are morphologically distinct based on gill raker counts, the clustering of two specimens of S. jussieu with S. fimbriata could be due to introgressive hybridization. COI sequences of S. atricauda and S. melanura from GenBank are identical. Interspecific genetic distances between some pairs of marine Sardinella are very low (0-1.6%). Further taxonomic studies using other mitochondrial and nuclear regions should be done to differentiate one species from the other and to establish their evolutionary relationships.
Article title: DNA barcoding of fishes of Laguna de Bay, Philippines
Authors: Luis Miguel Aquino, Jazzlyn M. Tango, Reynand Jay C. Canoy, Ian Kendrich C. Fontanilla, et al.
Publication title: Mitochondrial DNA 22(4): 143-53, August 2011
Laguna de Bay, the largest lake in the Philippines, is an important part of the country's fisheries industry. It is also home to a number of endemic fishes including Gobiopterus lacustris (Herre 1927) of family Gobiidae, Leiopotherapon plumbeus (Kner 1864) of family Terapontidae, Zenarchopterus philippinus (Peters 1868) of family Hemiramphidae and Arius manillensis Valenciennes 1840 of family Ariidae. Over the years, a steady decline has been observed in the abundance and diversity of native fishes in the lake due to anthropogenic disturbances. In this study, a total of 71 specimens of 18 different species belonging to 18 genera, 16 families, and seven orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. All of the fish species were discriminated by their COI sequences and one endemic species G. lacustris, showing deep genetic divergence, was highlighted for further taxonomic investigation. Average Kimura 2-parameter genetic distances within species, family, and order were 1.33%, 18.91%, and 24.22%, respectively. These values show that COI divergence increases as taxa become less exclusive. All of the COI sequences obtained were grouped together according to their species designation in the Neighbor-joining tree that was constructed. This study demonstrated that DNA barcoding has great potential as a tool for fast and accurate species identification and also for highlighting species that warrant further taxonomic investigation.
Full text available upon request to the author
Article title: DNA barcoding of the ichthyofauna of Taal Lake, Philippines
Authors: Sean V. L. Aquilino, Jazzlyn M. Tango, Ian Kendrich C. Fontanilla, Roberto Pagulayan, et al.
Publication title: Molecular Ecology Resources 11(4): 612-9, July 2011
This study represents the first molecular survey of the ichthyofauna of Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal Lake, the third largest lake in the Philippines, is considered a very important fisheries resource and is home to the world's only freshwater sardine, Sardinella tawilis. However, overexploitation and introduction of exotic fishes have caused a massive decline in the diversity of native species as well as in overall productivity of the lake. In this study, 118 individuals of 23 native, endemic and introduced fishes of Taal Lake were barcoded using the partial DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene. These species belong to 21 genera, 17 families and 9 orders. Divergence of sequences within and between species was determined using Kimura 2-parameter (K2P) distance model, and a neighbour-joining tree was generated with 1000 bootstrap replications using the K2P model. All COI sequences for each of the 23 species were clearly discriminated among genera. The average within species, within genus, within family and within order percent genetic divergence was 0.60%, 11.07%, 17.67% and 24.08%, respectively. Our results provide evidence that COI DNA barcodes are effective for the rapid and accurate identification of fishes and for identifying certain species that need further taxonomic investigation.
Full text available upon request to the author
Article title: DNA barcodes of Philippine accipitrids
Authors: Perry S. Ong, Adrian U. Luczon, Jonas Quilang, Anna Mae Tatoy Sumaya, et al.
Publication title: Molecular Ecology Resources 11(2): 245-254, March 2011
DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae.
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Article title: DNA barcodes of the suckermouth sailfin catfish Pterygoplichthys (Siluriformes: Loricariidae) in the Marikina River system, Philippines: Molecular perspective of an invasive alien fish species
Authors: Joycelyn Cagatin Jumawan, Benjamin Vallejo, Corazon Buerano, Annabellee Herrera, et al.
Publication title: Journal of Materials Science Letters 4(2): 103-113, 2011
DNA barcoding for accurate identification of invasive alien fish species is relatively unexplored. In this study, partial sequence (655 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) was used to delineate between two species of exotic suckermouth sailfin catfish Pterygoplichthys – P. pardalis and P. disjunctivus and their intergrades, which dominate the ichthyofauna of the Marikina D River system, Philippines. Individuals were assigned to groups using an abdominal pattern scheme, and COI gene sequence divergence analysis was determined using Kimura 2-parameter distances. Results revealed two major clusters which were inconsistent with the abdominal pattern categories and were characterized by low genetic divergence (mean 0.2%); one cluster having shared genealogy of individuals pre-identified as P. pardalis and the intergrades, and another consisting mostly of P. disjunctivus. From the samples, six haplotypes with low genetic divergence (mean 0.5%) were identified, suggesting that the haplotypes belong to a single species despite abdominal pattern variations. Overall, the DNA barcodes do not complement the morphology-based identification of the two species in the river system. The results support the possibility of introgressive hybridization between P. pardalis and P. disjunctivus and the need to reassess taxonomic assignment of the two species using abdominal patterns as basis for species distinction. It is recommended that multiple molecular tools be used in future studies and that native Pterygoplichthys species and other hypostomine loricariids be subjected to DNA Vol. 4 | No. 2 | 2011 Philippine Science Letters 103
Article title: Geometric Morphometric Analysis and Gill Raker Count Variation of Populations of the Endemic Philippine Silver Perch, Leiopotherapon plumbeus (Perciformes: Terapontidae)
Authors: Brian S. Santos, Ian Kendrich C. Fontanilla, Jonas Quinalang
Publication title: Philippine Agricultural Scientist 93(4), December 2010
Geometric morphometrics has been applied in various studies to determine shape variation in fish populations. In this study, landmark-based geometric morphometrics was used to examine shape variation in native and translocated populations of Leiopotherapon plumbeus (Kner, 1864), an endemic and economically important fish in the Philippines. A total of 844 specimens were collected from seven localities, namely, Laguna de Bay (Binangonan and Tanay areas), Sampaloc Lake, Taal Lake, Paoay Lake, Maasin River in Candaba Swamp, and Lake Buhi. L. plumbeus in Taal Lake, Sampaloc Lake and Lake Buhi were transplanted from Laguna de Bay, whereas those in Laguna de Bay, Paoay Lake and Maasin River were native to these areas. Shape variation in the samples was greatest in the head, followed by the body depth. Specimens from the Binangonan and Tanay areas of Laguna de Bay were the most similar morphologically. Specimens from Paoay Lake were the most distinct which could be due to the geographic isolation of L. plumbeus in this lake from all the other populations. Variation in gill raker count, the most discriminating meristic trait in a previous study, was also determined. Specimens from Binangonan and Tanay had the most number of gill rakers, whereas those from Paoay had the least. Variations in body shape and gill raker counts could be due to differences in feeding lifestyles in different habitats as well as differences in physico-chemical characteristics of the water bodies. Further studies are needed, however, to verify these findings and to determine the physico-chemical as well as genetic factors that could have contributed to such variation.
Article title: Survey and spatial distribution of shoreline malacofauna in Grande Island, Subic Bay
Authors: Gizelle Batamalaque and Ian Kendrich C. Fontanilla
Publication title: Philippine Journal of Science 139(2): 149-159, December 2010
Grande Island, Subic Bay is an excellent site for studying spatial distributions on a local scale because of its topographic heterogeneity. This study aimed to provide a systematic survey and spatial distribution of shoreline malacofauna of the island using a total of 956 continuous 2 x 2 m plots. Substrate types were classified as sand, sand-pebble, rock-sand, rock-pebble, pebble-rock-coral rubble, boulder, and wood. One hundred mollusk species were identified from 44, 465 individuals with 54 additional individuals still unresolved. Mollusks were found to be distributed according to the substrate type (composition and particle size) and are independent of the total area sampled. Substrates that are loose or unstable tend to have only few species while those that are compact have more species. Only bivalves were found in the sand substrate. Planaxids, nerites, trochids, and siphonarids were the dominant groups in substrates with rocks, pebbles, and coral rubble. Nudibranchs only occurred in rocky substrates. Nacellids and littorinids predominate particularly in boulders. Littorinids were also numerous in woody substrates. Juvenile trochids and planaxids were most abundant in regions with calm water while Cellana species and adult trochids were particular in areas exposed to strong currents. The morphological adaptations of different species enabled them to occur in specific habitat types.
Article title: The new family Diapheridae, a new species of Diaphera Albers from Thailand, and the position of the Diapheridae within a molecular phylogeny of the Streptaxoidea (Pulmonata: Stylommatophora)
Authors: Jirasak Sutjarit, Fred Naggs, Christopher M. Wade, Ian Kendrich C. Fontanilla
Publication title: Zoological Journal of the Linnean Society 160(1): 1-16, August 2010
The Streptaxoidea are an ancient and species diverse group that is poorly understood. Examination of the reproductive anatomy of Diaphera showed it to be notably distinct from that of most other streptaxid genera but to exhibit similarities with the reproductive anatomy of Sinoennea (Enneinae), Careoradula (Strepaxinae), Discartemon (Strepaxinae), Augustula (Strepaxinae), and a species of Imperturbatia (Gibbinae). Our molecular phylogenetic analysis placed the two genera with high-spired shells, Sinoennea and Diaphera, in an isolated position as a sister group to the Streptaxidae sensu stricto. This basal divergence within the Streptaxoidea provides support to the proposed recognition of a new family, the Diapheridae. None of the genera possessing low-spired shells, Careoradula, Discartemon, Augustula, and Imperturbatia, were available for inclusion in the molecular analysis and we therefore provisionally restrict the Diapheridae to Diaphera and Sinoennea. However, based on their reproductive anatomy Careoradula, Discartemon, Augustula and a species of Imperturbatia may cluster with the Diapheridae when included in a molecular analysis.© 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160, 1–16.
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Article title: The small subunit (SSU) ribosomal (r) RNA gene as a genetic marker for identifying infective 3rd juvenile stage Angiostrongylus cantonensis
Authors: Ian Kendrich C. Fontanilla and Christopher M. Wade
Publication title: Acta Tropica 105(2): 181-6, March 2008
We have developed a molecular method using PCR-direct sequencing to identify the infective 3rd juvenile stage of Angiostrongylus cantonensis, a nematode parasite of rodents that can accidentally infect humans and cause eosinophilic meningitis. We demonstrate that the 5' end of the small subunit (SSU) ribosomal (r) RNA gene is a suitable marker to identify A. cantonensis and distinguish it from other closely related Angiostrongylus species. When the SSU rRNA marker was employed on nematode populations extracted from the black slug Laevicaulis altae collected in 2 test sites in the Philippines, the infective 3rd juvenile stage A. cantonensis was detected without difficulty. The phylogenetic position of other non-angiostrongylid nematodes isolated was also determined. The molecular technique developed in this study provides a rapid and accurate method for the identification of A. cantonensis when morphological identification proves difficult or inadequate.
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