Background: In sexual assault casework, the detection of semen on a sample supports an allegation of sexual contact and indicates the presence of DNA from a male source. Ideally, techniques employed should demonstrate high sensitivity and specificity and should be compatible with standard DNA typing procedures. To contribute recommendations for routine DNA tests of sexual assault cases in the Philippines, we evaluated the RSID TM-Semen, an immunochromatographic test for human semenogelin (Sg), in parallel with the alternate light source (ALS) method using Mini BLUMAXX™ III and the acid phosphatase (AP) test using Seminal Fluid DISCHAPS TM. Results: The ALS detected semen diluted until 5% (v/v) fluid, whereas the AP assay was sensitive down to 0.5% (v/v). Non-blood-containing stains were visible under blue light except on dark-colored cloth. All semen-containing fluids including post-ejaculatory urine tested positive for AP and Sg. RSID TM-Semen was sensitive down to 0.5 nL of semen; did not cross-react with blood, saliva, and female urine; and successfully detected Sg on the majority of post-coital samples tested. Complete short tandem repeat (STR) profiles of the semen donors were generated for most samples incubated in the RSID TM-Universal Buffer (UB). However, we report an extraction efficiency of 15% for UB which can lead to partial profiles in already compromised samples. Conclusion: We recommend the use of ALS in visualizing stains present on surfaces and the AP test on bloodstained materials. These presumptive tests should be followed by RSID TM-Semen test to confirm the presence of semen prior to DNA profiling.

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In the Philippines, more than 7000 cases of sexual assault are reported annually. DNA technology is a powerful tool in identifying assailants. However, it is not routinely used in sexual assault investigations due to insufficient government support to cover the high cost of DNA testing and the absence of a national system for sample collection, handling, storage, and DNA testing of biological evidence. In itself, the nature of sexual assault samples containing DNA mixtures presents challenges to laboratory methods and interpretation of results. The sample recovered from the victim may only contain trace amounts of the assailant’s DNA, may have degraded due to prolonged storage in ambient conditions which is warm and humid in the tropics, or contaminated with inhibitors, such as in anal swabs. Hence, a closer evaluation of the processes of evidence collection and DNA testing is needed to increase the likelihood of success in generating conclusive results. In this paper, we propose an integrated system for DNA testing of biological samples collected from sexual assault victims considering the limitations of resources and the prevailing warm climate. Recommendations in this work should provide basis for formulating national guidelines for DNA analysis in aid of criminal investigations. The proposed scheme can be adopted by forensic DNA laboratories in the Philippines and in other countries facing similar challenges.

The Formosan wild boar () is an endemic subspecies in Taiwan. Understanding the origins and spread of the Formosan wild boar could help clarify East Asian wild boar dispersion. Although in situ domestication of the wild boar occurred at a number of domestication centers across East Asia, corroborating archaeological and genetic evidence of pig domestication on Taiwan is lacking, leading to domestication being described as cryptic. This characterization applies to the Lanyu pig-a domestic pig breed found on Taiwan. To better understand pig domestication, this study examines the sympatric Formosan wild boar and domestic Lanyu pig to build a model of potential wild boar domestication on Taiwan and elucidate wild boar domestication patterns in the region. To this end, a comprehensive phylogenetic study of the Formosan wild boar and the Lanyu pig was conducted on animals sourced from Taiwan, Lanyu, and the Philippines. Phylogenetic analyses were conducted using full mitochondrial control-region sequences from 345 wild boars and domestic pigs. These were studied in concert with existing reports on 206 Asian wild boars. Genetic characteristics and Bayesian phylogenetic tree results identified 2 wild boar lineages of remote phylogenetic relationship. These were Formosan wild boar lineage (FWBL) and Formosan wild boar with Lanyu sign lineage (FWBLYL). Molecular clock analyses indicate that FWBLYL diverged earlier than other insular East Asia wild boars and show that FWBLYL and FWBL diverged approximately 0.60 million years ago. This result supports boars of FWBLYL being the earliest wild boars to have spread and become isolated in insular East Asia. In addition, the study proposes 6 Asian wild boar dispersion routes during glacial periods. At least 3 of these events occurred in insular East Asia with subsequent geographical isolation after glacial recession. This isolation potentially led to allopatric differentiation of wild boar subspecies. Also, the similar genetic signature and phylogenetic uniqueness of Lanyu pigs to wild boars of FWBLYL suggests such wild boars were the wild ancestor of domestic Lanyu pigs. This result indicates potential in situ domestication occurring on Taiwan. Finally, pigs possessing FWBLYL's genetic signatures were continuously distributed among Taiwan, Lanyu, and the Philippines. This pattern may signify human-mediated pig dispersal routes.

The coconut is a major crop of many tropical countries, with the endosperm being one of its main products. The coconut soft-endosperm variants, the Makapuno and the Lono, are emerging as economically important. This review describes this crop, its salient endosperm phenotypes and the prevailing hypotheses associated with these. We also collate the literature on the Makapuno and provide a comprehensive review of the scarce information on the Lono. We review the current tenets of plant DNA methylation and provide examples of altered phenotypes associated with such methylation changes. We explore how the changes in the methylome affect endosperm development and the tissue culture process. We further cite the epigenetic basis of an altered endosperm phenotype of a closely related species to the coconut, the oil palm. We discuss how such modifications could affect coconut endosperm development, yielding the Makapuno and Lono phenotypes.

This study determined the relative abundance of Cebu black shama (Copsychus cebuensis Steere) in selected isolated forest fragments in Cebu Island, Philippines and their genetic diversity based on 619 bp cytB gene. Mist nets were used to capture the bird in these forest fragments. Four contour feathers were plucked from the body of the caught birds, before they were released, and were stored in tubes with 70% ethanol before DNA extraction. Fifty-nine black shama (C. cebuensis) individuals were encountered from the visited territories. At least 13 black shama individuals were estimated to inhabit one hectare of forest habitat. For the first time, analyses of mitochondrial genes revealed that C. cebuensis had a long evolutionary history from an initially large and stable population that went through recent expansion resulting from a recent isolating or bottleneck event as indicated by high haplotype diversity (Hd) and nucleotide diversity (πn), i.e. Hd>0.50 and πn>0.005, and non-significant values of Tajima’s D test, Fu and Li’s D*, and Fu’s Fs statistics. It is hypothesized that this bottleneck event was habitat fragmentation. Furthermore, phylogenetic analyses of C. cebuensis supported its monophyly.

Appropriate decision‐making in conservation programmes requires an understanding of the population genetic structure of various indigenous species. However, in lake and river ecosystems rated as biodiversity conservation priority areas in the Philippines, the diversity of many species remains uncharacterized.To address the existing gap, genetic diversity of two native freshwater fishes, Glossogobius celebius (Valenciennes, 1837) and Glossogobius giuris (Hamilton, 1822) was measured. Genetic structure and estimates of genetic variation for each species was determined using isozyme analysis.A higher level of genetic variation was observed within G. celebius populations compared with G. giuris. Genetic structure indicated that the observed genetic variation in G. giuris is due to the variation among the populations. The results suggest the presence of geographical barriers even in adjacent aquatic ecosystems that could restrict gene flow among G. giuris populations.This study supports the need for immediate conservation interventions for both species as they show a low level of genetic diversity in addition to being threatened in their own environment. Possible measures include translocation and establishment of a refuge population of the species studied to be complemented with location‐specific strategies that would enhance their habitat conditions. In addition, education and enhancing the awareness of the local community regarding habitat protection are strongly recommended. Copyright © 2014 John Wiley & Sons, Ltd.

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