Microclimate and Physiological Effects in the Roosts of Cave Dwelling Bats: Implications in the roost selection and the conservation in Sarawak, Malaysian Borneo

As a species, bats play a crucial part in both ecological and economic roles. However, this group of mammals is largely threatened due to anthropogenic activities either inside or around their caves. In this study, we investigate the effects of cave microclimate and physiological parameters on bat roost preference in Fairy Cave Nature Reserve (Fairy Cave NR). The microclimate and physiological parameters including temperature (°C), relative humidity (RH), light intensity (lux), air flow, passage dimension (m), roost height (m) and distance of roost from nearest entrance (m) were measured. Results showed that Emballonura monticola, Hipposideros diadema, Hipposideros larvatus and Penthetor lucasi were roosting in Fairy Cave NR. These bats can be distinguished by their colony size, roost posture, spatial arrangement and position of their roost. Penthetor lucasi makes up the largest colony in the bright zone, whereas E. monticola has the smallest colony occupying the twilight zone throughout the cave. Members from the family Hipposideridae roost in the dark portion of the cave with zero light intensity. Emballonura monticola utilizes the hottest roost in the cave compared to the other microbats, whereas H. diadema inhabits the coolest roost. Physiological parameters such as light intensity, passage dimension and distance from nearest entrance are significant parameters in roosting preferences. These parameters should be monitored to ensure the sustainability of not only the aforementioned species, but also other species that roost in nearby caves of Bau limestone. (Wind Cave Nature Reserve- recorded with 13 species)

Do Time, Heterochromatin, NORs, or Chromosomal Rearrangements Correlate with Distribution of Interstitial Telomeric Repeats in Sigmodon (Cotton Rats)?

We studied the chromosomal distribution of telomere repeats (TTAGGG)n in 8 species of Sigmodon (cotton rats) using chromosome paints fluorescent in situ hybridization (FISH) from Sigmodon hispidus. In 2 species with the proposed primitive karyotype for the genus, telomere repeats were restricted to telomeric sites. But in the other 6 species that include 3 with proposed primitive karyotypes and 3 with highly rearranged karyotypes, telomere repeats were found on both telomeric sites and within interstitial telomeric sites (ITSs). To explain the distribution of ITS in Sigmodon, we gather data from C-bands, silver nitrate staining, G-bands, and chromosomal paint data from previous published studies. We did find some correlation with ITS and heterochromatin, euchromatic chromosomal rearrangements, and nucleolar organizing regions. No one type of chromosomal structure explains all ITS in Sigmodon. Multiple explanations and mechanisms for movement of intragenomic sequences are required to explain ITS in this genus. We rejected the hypothesis that age of a lineage correlates with the presence of ITS using divergence time estimate analyses. This multigene phylogeny places species with ITS (S.arizonae, S. fulviventer, S. hispidus, S. mascotensis, S. ochrognathus, and S. toltecus) in the clade with a species without ITS (S. hirsutus). Lineages with ITS (S. arizonae and S. mascotensis) arose independently from a lineage absent of ITS (S. hirsutus) around 0.67 to 0.83 Ma. The rearranged karyotypes of S. mascotensis and S. arizonae appear to be an independently derived autapomorphic characters, supporting a fast rate of chromosomal changes that vary among species

Microsatellite DNA polymorphism of Macaca fascicularis populations in Malaysia

A total of 386 long-tailed macaques (M. fascicularis) from 17 populations in Malaysia was analysed using eight polymorphic microsatellite loci on a microfluidic-based platform (Agilent DNA 1000 Chips on the Agilent 2100 bioanalyzer) to identify and evaluate the genetic polymorphism and population structure. The microfluidic-based chip platform provides simple, reliable and cost effective approach for microsatellite studies. Genetic diversity estimates showed that the Peninsular Malaysian populations are slightly more diverse than their Bornean conspecifics. Furthermore, weak population structuring among the peninsula populations suggest that they comprise of genetically contiguous populations. The Sarawak and Labuan populations were differentiated from the peninsula populations except for the Sabah population which is due to the low sample number from the latter. Interestingly, no matching genotype was found among all samples indicating that the loci set can be used for individual identification of M. fascicularis

Western Tarsier Cephalopachus bancanus at Matang Wildlife Centre, Sarawak

The huge, forward-facing eyes, large ears and small body size immediately identify this animal as a tarsier. The Western Tarsier Cephalopachus bancanus is the only species currently recognized on the island of Borneo: it mainly inhabits lowland areas, but there are montane records up to 1200 metres elevation

Genetics Diversity of Captive and Semi-Wild Orangutan in Malaysia

Orangutan is known to be genetically diverse than any other primates in the world. There are three species of Orangutan namely Pongo abelii, Pongo tapanuliensis and Pongo pygmaeus. The Bornean Orangutan, P. pygmaeus were further diverged into three subspecies, namely P. p. pygmaeus, P. p. wurmbii and P. p. morio. The wild populations are highly endangered due to habitat loss and hunting. As a result, all the species and subspecies of Orangutan were declared as critically endangered. Orangutans are also being kept in numerous captive and semi-wild centres around the world. However, not much data is available in term of genetic diversity of these Orangutan in captive and semi-wild facilities in Malaysia which is important for its management. This is because, each species as well as subspecies of Orangutan are geographically isolated in the wild. Further, studies have shown significant genetic differences among them. Therefore, it is critical to genetically assess all Orangutan in captive to maintain their species/subspecies genetic integrity. We used non-invasive samples from five captive and two semi-wild centres in Malaysia. The genetic diversity of Orangutan was determined using both mitochondrial protein coding (NADH Dehydrogenase Subunit 5) and non-coding (Hypervariable Region 1) DNA. Results revealed high genetic diversity among all the Orangutan in captive and semi-wild centres in Malaysia. Several misclassifications of Orangutan species and subspecies were also detected. However, all those misclassifications were resolved through our phylogenetic data with high confidence. Moreover, we have provided reliable species and subspecies information for all the Orangutans involved in this study

Bioacoustic Study of Insectivorous Bats

The microbat has developed advanced echolocating ability compared to the megabats or old-world fruit bats that relies mainly on vision and olfaction for food hunting. The microbats orient and capture their prey by means of echolocation that involves ultrasonic calls >20kHz, in which a frequency beyond the range of human hearing. Their morphological features and echolocation calls are designed in correlate with their adaptability with the environment especially with their superiority maneuver, detection and localize targeted object in cluttered environment. In Borneo, there are a total of 100 bats’ species with 85 species from Sarawak (15 Megabats and 70 echolocating microbats). The use of ultrasonic detectors in monitoring echolocation calls by using bat detectors has surged the researchers’ interest to study on bats and their habitat relationship as well as addressing questions concerning their activity patterns despite the limitations in this method. Present study intends to build a call library comprising of different species call frequencies as well as bat activity patterns in Kubah National Park via acoustic measures. To date, higher elevations recorded the highest activity that is determined by the number of passes but lower by species richness as compared to the lower elevation. Acoustic monitoring provides additional data of bat species that occur at each elevation that were not caught during trapping. These data will be highly useful in studying effect of landscape changes in the future

Detection of novel coronaviruses from dusky fruit bat (Penthetor lucasi) in Sarawak, Malaysian Borneo

Background: Sarawak has one of the highest diversity of fruit bats species (family Pteropodidae) in Malaysia, with 19 species described. Most coronavirus (CoV) studies have mainly focused on insectivorous bats, resulting in a lack of information on CoVs present in frugivorous bats. In addition, bat CoV surveillance activities are lacking in Malaysia. Objectives: Our study focuses on determining the presence of bat CoVs in dusky fruit bat (Penthetor lucasi). Methods: Guano samples belonging to P. lucasi were collected from Wind Cave Nature Reserve. The samples were screened for the presence of CoVs using validated heminested consensus RNA-dependent RNA polymerase consensus primers. Results: The bat CoV positivity rate was 38.5% (n = 15/39), with the viruses belonging to two subgenera: Alphacoronavirus (α-CoV) and betacoronavirus (β-CoV). Phylogenetic analysis revealed that CoVs from 14 samples of P. lucasi belong to the genus α-CoV and may represent previously described genetic lineages in insectivorous bats in Wind Cave. However, only one sample of P. lucasi was detected with β-CoV which is closely related to subgenus Nobecovirus, which is commonly seen in frugivorous bats. Conclusions: This study provides the first available data on CoVs circulating in P. lucasi

Phylogenetic relationships and morphological variation of gymnures (Galericidae: Hylomys) from Genting Highlands, Pahang, Malaysia

Gymnures from the genus Hylomys are widely distributed across Sundaland and the Indochinese region. However, the relationships among its members in Peninsular Malaysia especially from Genting Highlands are still lacking. This study aims to examine the morphology and genetically analyse of the Hylomys specimens collected from the new isolated population of Genting Highlands, Pahang, Malaysia. Morphometric analyses showed that morphological variation exists among the Hylomys lineage. The external morphology and the skull measurements of the taxa studied coincide with those of Hylomys maxi from Peninsular Malaysia and Sumatra based on descriptive statistics and principal component analysis (PCA). The differences within the Hylomys taxa are also evident in the phylogenetic tree and K2P genetic distances analyses inferred from cyt b. Hylomys samples from Genting Highlands formed a clade with H. maxi from Cameron Highlands and Fraser’s Hill, Peninsular Malaysia and Sumatra. However, they were separated from Hylomys parvus (Sumatra), Hylomys suillus (Java) and Hylomys dorsalis (Borneo). Relatively, low genetic distances were detected among the studied taxa with other H. maxi (<6% K2P distance) while high genetic distances were observed when compared to other Hylomys taxa (>18.0% K2P distance). Based on these facts, we confirm that the gymnures from Genting Highlands belong to a valid species, Hylomys maxi along with other Peninsular Malaysia samples based on genetics and morphological data which probably originated from Sumatra a long time ago

Genetic diversity of the cave roosting dusky fruit bat, Penthetor lucasi from Sarawak

Previous studies have revealed a high genetic divergence in Penthetor lucasi population in Sarawak, indicating it may consist of multiple genetic lineages. However, these studies are not accompanied by morphological data from the studied population suggesting this may be an effect of isolation by distance, especially with small sampling coverage. Here, we provide information based on D-loop sequence analysis from 32 individuals of Penthetor lucasi collected from four different regions in Sarawak. Our results revealed a high haplotype diversity and low nucleotide diversity, suggesting that these populations are possibly recovering from a recent geological and climatic event. However, neutrality test and mismatch distributions showed longterm population stability with no population subdivision observed among the studied populations. The moderate to high level of gene flow found in this study indicates that Penthetor lucasi population is likely panmictic. Meanwhile, the low level of genetic divergence value among and within populations could account for the absence of species complexity in this study. Our result highlighted the importance of sampling coverage in proper assessment of species diversity especially in species with wide distribution

Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo

Objective: Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at − 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidi‑ rectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed. Results: CoV-RNA was detected in ten specimens (47.6%, n =21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses. Keywords: Bat, Cave, Coronavirus, Guano, Sarawa