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Fulltext Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target

Lee PS, Sing KW, Wilson JJ

PLoS One, 2015;10(4):e0123871.
PMID: 25898278 DOI: 10.1371/journal.pone.0123871

Most tropical mammal species are threatened or data-deficient. Data collection is impeded by the traditional monitoring approaches which can be laborious, expensive and struggle to detect cryptic diversity. Monitoring approaches using mammal DNA derived from invertebrates are emerging as cost- and time-effective alternatives. As a step towards development of blowfly-derived DNA as an effective method for mammal monitoring in the biodiversity hotspot of Peninsular Malaysia, our objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment (ii) to design and test primers that can selectively amplify mammal COI DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The persistence period of amplifiable mammal mtDNA in blowfly guts was 24 h to 96 h post-feeding indicating the need for collecting flies within 24 h of capture to detect mammal mtDNA of sufficient quantity and quality. We designed a new primer combination for a COI DNA mini-barcode that did not amplify blowfly DNA and showed 89% amplification success for a dataset of mammals from Peninsular Malaysia. The short (205 bp) DNA mini-barcode could distinguish most mammal species (including separating dark taxa) and is of suitable length for high-throughput sequencing. Our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring.
Application of DNA barcodes in wildlife conservation in Tropical East Asia

Wilson JJ, Sing KW, Lee PS, Wee AK

Conserv Biol, 2016 10;30(5):982-9.
PMID: 27341687 DOI: 10.1111/cobi.12787

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.
Male fetuses are associated with increased risk for cesarean delivery in Malaysian nulliparae

Viegas OA, Lee PS, Lim KJ, Ravichandran J

Medscape J Med, 2008;10(12):276.
PMID: 19242582

The association between fetal sex and outcome of pregnancy and labor has been well documented in western populations. However, no studies in Malaysia or other developing countries have examined the effect of fetal sex on such outcomes.The main objective of this study was to determine the influence of fetal sex on the outcome of labor at term in a cohort of Malaysian nulliparae.A retrospective observational study was designed using data from 4644 Malaysian nulliparae who gave birth consecutively to singleton male babies at Hospital Sultanah Aminah, Johor Bahru, after normal full-term pregnancies.The results of this study indicate that mothers giving birth to male infants have a greater risk of requiring cesarean delivery because male babies are heavier and have statistically significantly greater head circumference (P < .001). These findings concur with those obtained in western populations and suggest that the differences in outcome observed are biological, not dictated by race, ethnicity, or environmental conditions. Such information could help in the antenatal assessment of Malaysian patients and stimulate more comprehensive studies of the mechanisms involved in this sex-based difference in outcomes. Reasons for such differences are proposed.
Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Lee PS, Gan HM, Clements GR, Wilson JJ

Genome, 2016 May 11.
PMID: 27696907

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.
DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ

Bull. Entomol. Res., 2015 Dec;105(6):717-27.
PMID: 26344799 DOI: 10.1017/S0007485315000681

Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.
Fulltext Standardization and experience may influence the survival of laparoscopic radical hysterectomy for cervical cancer

Lee CL, Huang KG, Chua PT, Mendoza MCVR, Lee PS, Lai SY

Taiwan J Obstet Gynecol, 2021 May;60(3):463-467.
PMID: 33966729 DOI: 10.1016/j.tjog.2021.03.013

OBJECTIVE: Minimally invasive radical hysterectomy has been shown to be associated with poorer outcome in an influential prospective, randomized trial. However, many centers worldwide performing minimally invasive radical hysterectomy have data and experience that prove otherwise. We aim to review surgical and oncologic outcomes of patients operated by Laparoscopic Radical Hysterectomy in a tertiary hospital, by experienced surgeons and standardization in radicality, for cervical carcinoma Stage 1A1-1B1 from January 2009 to May 2014.
MATERIALS & METHODS: Standardised surgical technique with Parametrium & Paracolpium resection approach was adopted by qualified and experienced Gynecologic/Gyne-Oncologic Endoscopic & Minimally Invasive Surgeons in performing Laparoscopic Radical Hysterectomy for Cervical Cancer stage 1A1-1B1 from January 2009-May 2014, involving 53 patients. Electronic Medical Record system (EMR) Of Chang Gung Memorial Hospital(Tertiary Referral Centre), Department of Obstetrics & Gynecology was accessed for surgical and oncologic outcomes.
RESULTS: Fifty-Three patients operated from January 2009 to May 2014 were followed up for an average of 96.7 months with longest follow-up at 127 months. There were no cases of recurrence or death reported. 5 Year - Survival Rate and 5 Year Disease-Free Survival Rate were 100%. Two patients received post-operative pelvic radiation concurrent with chemotherapy using Cisplatin due to greater than 1/3 cervical stromal invasion.
CONCLUSION: It is vital to standardize minimally invasive surgical techniques for early stage cervical cancer, with focus on adequate radicality and resection which may contribute to excellent survival outcomes. Further international multi-center randomized trial (Minimally Invasive Therapy Versus Open Radical Hysterectomy In Cervical Cancer) will provide justification for continued practice of MIS in early stage cervical cancer.
DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines

Casas PAS, Sing KW, Lee PS, Nuñeza OM, Villanueva RJT, Wilson JJ

Mitochondrial DNA A DNA Mapp Seq Anal, 2018 03;29(2):206-211.
PMID: 28155593 DOI: 10.1080/24701394.2016.1267157

Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
Blowfly-derived mammal DNA as mammal diversity assessment tool: Determination of dispersal activity and flight range of tropical blowflies

Lee PS, Dong MH, Yan XL, He TY, Yu SF, Wee SL, et al.

Biodivers Data J, 2023;11:e108438.
PMID: 37736305 DOI: 10.3897/BDJ.11.e108438

Mammalian DNA extracted from the invertebrates, especially blowfly-derived DNA, has been suggested as a useful tool to complement traditional field methods for terrestrial mammal monitoring. However, the accuracy of the estimated location of the target mammal detected from blowfly-derived DNA is largely dependent on the knowledge of blowflies' dispersal range. Presently, published data on adult blowfly dispersal capabilities remain scarce and mostly limited to temperate and subtropical regions, with no published report on the adult blowfly dispersal range in the Tropics. We seek to determine the blowfly flight range and dispersal activity in a tropical plantation in Malaysia by mark-release-recapture of approximately 3000 wild blowflies by use of rotten fish-baited traps for nine consecutive days. Out of the 3000 marked Chrysomya spp., only 1.5% (43) were recaptured during the 9-day sampling period. The majority of the blowflies (79%) were recaptured 1 km from the release point, while 20.9% were caught about 2-3 km from the release point. One individual blowfly travelled as far as 3 km and before being recaptured, which was the maximum dispersal distance recorded in this study. This result suggests that the estimated locations of the mammals detected from blowfly-derived iDNA is likely to be within 1-2 km radius from the origin of the blowfly sampling location. However, a more accurate estimated distance between the target mammal and the blowfly sampling location requires further investigation due to various factors, such as blowfly species, wind speed and direction that may potentially affect the blowfly dispersal activities. This study contributes further understanding on the development of a blowfly-derived DNA method as a mammalian monitoring tool in the tropical forests.
Diversity and human perceptions of bees (Hymenoptera: Apoidea) in Southeast Asian megacities

Sing KW, Wang WZ, Wan T, Lee PS, Li ZX, Chen X, et al.

Genome, 2016 Oct;59(10):827-839.
PMID: 27327818

Urbanization requires the conversion of natural land cover to cover with human-constructed elements and is considered a major threat to biodiversity. Bee populations, globally, are under threat; however, the effect of rapid urban expansion in Southeast Asia on bee diversity has not been investigated. Given the pressing issues of bee conservation and urbanization in Southeast Asia, coupled with complex factors surrounding human-bee coexistence, we investigated bee diversity and human perceptions of bees in four megacities. We sampled bees and conducted questionnaires at three different site types in each megacity: a botanical garden, central business district, and peripheral suburban areas. Overall, the mean species richness and abundance of bees were significantly higher in peripheral suburban areas than central business districts; however, there were no significant differences in the mean species richness and abundance between botanical gardens and peripheral suburban areas or botanical gardens and central business districts. Urban residents were unlikely to have seen bees but agreed that bees have a right to exist in their natural environment. Residents who did notice and interact with bees, even though being stung, were more likely to have positive opinions towards the presence of bees in cities.
Fulltext Citizen Science: The First Peninsular Malaysia Butterfly Count

Wilson JJ, Jisming-See SW, Brandon-Mong GJ, Lim AH, Lim VC, Lee PS, et al.

Biodivers Data J, 2015.
PMID: 26751033 DOI: 10.3897/BDJ.3.e7159

Over the past 50 years, Southeast Asia has suffered the greatest losses of biodiversity of any tropical region in the world. Malaysia is a biodiversity hotspot in the heart of Southeast Asia with roughly the same number of mammal species, three times the number of butterfly species, but only 4% of the land area of Australia. Consequently, in Malaysia, there is an urgent need for biodiversity monitoring and also public engagement with wildlife to raise awareness of biodiversity loss. Citizen science is "on the rise" globally and can make valuable contributions to long-term biodiversity monitoring, but perhaps more importantly, involving the general public in science projects can raise public awareness and promote engagement. Butterflies are often the focus of citizen science projects due to their charisma and familiarity and are particularly valuable "ambassadors" of biodiversity conservation for public outreach.
Fulltext Familiarity with, perceptions of and attitudes toward butterflies of urban park users in megacities across East and Southeast Asia

Lim VC, Sing KW, Chong KY, Jaturas N, Dong H, Lee PS, et al.

R Soc Open Sci, 2022 Nov;9(11):220161.
PMID: 36405642 DOI: 10.1098/rsos.220161

Perceptions of, and attitudes toward, wildlife are influenced by exposure to, and direct experiences with, nature. Butterflies are a conspicuous and ubiquitous component of urban nature across megacities that are highly urbanized with little opportunity for human-nature interactions. We evaluated public familiarity with, perceptions of and attitudes toward butterflies across nine megacities in East and Southeast Asia through face-to-face interviews with 1774 urban park users. A total of 79% of respondents had seen butterflies in their cities mostly in urban parks, indicating widespread familiarity with butterflies. Those who had seen butterflies also had higher perceptions of butterflies, whereas greater than 50% of respondents had positive attitudes toward butterflies. Frequent visits to natural places in urban neighbourhoods was associated with (i) sightings of caterpillars, indicating increased familiarity with urban wildlife, and (ii) increased connectedness to nature. We found two significant positive relationships: (i) between connectedness to nature and attitudes toward butterflies and (ii) between connectedness to nature and perceptions of butterflies, firmly linking parks users' thoughts and feelings about butterflies with their view of nature. This suggests that butterflies in urban parks can play a key role in building connectedness to nature and consequently pro-environmental behaviours and support for wildlife conservation among urban residents.

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