Biology subjects

Wibowo, A. A.

Publications and source records attributed to Wibowo, A. A..

17 recordsLinked to original sources

bioRxiv2021

Possible environmental and meteorological factors underlying scaly-breasted munia Lonchura punctulata (L.) mass mortality events in Southeast Asia urban and rural areas in September 2021

Mass bird mortality is a rare event. This event could be happened and could be a combination of numerous factors. It could be something thats still completely unknown to us. In September 2021 in SE Asia, there were 2 mass bird mortality events of Lonchura punctulata. The first event happens on 9 September in rural area at 08.00 AM and second happens on 14 September at 12.00 PM in urban area. The results show that precipitation combined with the wind gust might be correlated with mass mortality. The results showed precipitation factors have contributed 71.18% (R2 = 0.714, P = 0.008) to the mortality and followed by wind gust with 28.81% contribution (R2 = 0.41, P = 0.08). The meteorological parameter was not the only factors affecting the mortality events. The landscapes in urban and rural areas have experienced fragmentations. Urban areas have severe fragmentation of vegetation covers with remaining vegetation covers were only 17.4% and patch density indices of 0.29. In contrast rural areas still have higher vegetation cover remnants about 21.12% and patch density indices of 0.93. Then severe meteorological events combined with the fragmented habitats of L. punctulata may explain the mass mortality of this bird species.

ecology↗

bioRxiv2021

Modeling the underlying environmental factors of milky sea case and luminous bacteria presence in Java Southern Sea in 2019

The milky sea is one of the unique natural phenomena caused by the presence of luminous Vibrio bacteria in marine ecosystems. Recently a milky sea has been reported frequently included in the Java Southern Sea. Simultaneously, numerous remote sensing based approaches have been developed to detect the presence of luminous bacteria and the milky sea. Despite this state of the art, the information of detrimental factors of the marine bioluminescence was still limited. Then this research aims to model the underlying environmental factors causing the milky sea and luminous bacteria presence in the Java Southern Sea in 2019. The remote sensing assessment for the period of July 29-August 6, 2019 shows that the magnitude of bioluminescence measured in radiance was having a maximum value of 255 nanoW/cm2/sr and an average of 107 nanoW/cm2/sr/day (95%CI: 71.9 to 142 nanoW/cm2/sr/day). The milky sea size increased and reached its peak with a size of 44,124 km2 and then declined. The average milky sea size was 37,942 km2 (95% CI: 33,400 to 42,500 km2) and increased with average rate of 16.01% (95%CI: 5.41% to 26.66%). While Akaike Information Criterion (AIC) indicates that the best model to infer the relationship of bacterial bioluminescence with its environmental factors contained Chlorophyll a followed by sea surface temperature factors with AICc values of 101.16 (AICweight: 0.50) and 101.95 (AICweight: 0.34). This indicates that low temperature and high plankton cells is the limiting factors of the bacterial bioluminescence.

ecology↗

bioRxiv2021

Spatial modeling of extinct Southeast Asian Hobbit Homo floresiensis habitat suitability based on its diet availability and climatic parameters as a proxy

The discovery of a new prehistoric species of the genus Homo remains a significant matter of intense interest. One of significant discovery recently is the Homo floresiensis, representing a small-bodied and small-brained hominin, excavated, and found in Liang Bua Cave in Flores Island, East Nusa Tenggara, Indonesia. This species height was only about 106 cm (36") and the weight was 30-40 kg (66-86 lbs). H. floresiensis was known consumed extant murine rodents as its diets as this was evidence found in Liang Bua Cave. Then this study aims to model the H. floresiensis suitable habitat using maximum entropy method and 2 extant murine rodents, Rattus exulans and R. rattus as a proxy. The results show that the most suitable habitats for H. floresiensis indicated by suitable habitat values close to 1 were concentrated in the central of Flores Island that was overlapped with mountainous areas with elevation ranging from 1500 to 2000 m. These suitable habitats were also overlapped with dense vegetation covers, volcanic rock, and Kiro rock formation. Climatic parameters that limit the distributions of H. floresiensis were annual mean temperature, isothermality, minimum temperature of coldest period, and precipitation seasonality. Parts of Flores Island with the low temperature below 20 {degrees}C were favorable for H. floresiensis while an increase in isothermality limits the H. floresiensis distributions.

ecology↗

bioRxiv2021

Camera trap based niche partitioning model of medium size ungulates and its implications on tigers prey availability in SE Asian rainforest

The presence and survival of the Sumatran tiger were determined by the presence, density, and activity of its prey. Several medium size mammal belongs to the ungulate were known as the potential prey for the tiger. While, the information on the temporal availability of this prey in the rainforest is still limited. In here this study aimed to aims to model the niche partitioning of several mammalian species that was potential prey for tiger. The studied species were including barking deer (Muntiacus muntjak), bearded pig (Sus barbatus), and wild boar (Sus scrofa). The method was using camera trap with data analyses including the calculation of Kernel density, diel activity, and niche partitioning determined using overlap index. . Based on the results, barking deer and wild boar showed only singular activity peak while bearded pig has several activity peaks. Only wild boar showed a strict diurnal activity pattern between 06:00 h and 12:00 h. Barking deer showed a crepuscular behavior with several activities observed at 18:00 h. While bearded pig showed a nocturnal behavior and showed at least two peaks of activity, one between 09:00 to 13:00 and another between 18:00 to 24:00 h. Barking deer and bearded pig uses almost similar niches since those species have the highest overlap indices value equals 0.504(95%CI:0.193-0.824). The lowest overlap indices value was observed for barking deer and wild boar with overlap indice values of 0.032(95%CI:0.0-0.162). Considering the diurnal activity pattern of the tiger that is mostly active at day, then the available preys were either barking deer or bearded pigs. While since barking deer and bearded pigs were using the same niche, then there will be potential competition.

ecology↗

bioRxiv2021

Modeling habitat suitability of vulnerable Mollucan Babirusa Babyrousa babyrussa in small island of Buru, Indonesia

Babirusa is a mammal belongs to Suidae family. This mammal belongs to Babyrousa genus is known endemic to Indonesia. Recently there are 3 species of Babyrousa, one species is Babyrousa babyrussa, listed as Vulnerable on the IUCN Red List of Threatened Species. Babyrousa occurs in Indonesia on Sulawesi island, Togian, Sula islands, and Taliabu, Mangole and Buru islands in the Molucca regions. The Moluccan Babirusa is now restricted to upland forests and mountainous terrain. Then this study aims to assess the suitability of Buru island as habitat for Moluccan Babirusa. The suitability analysis was based on GIS analysis using 4 determinant environmental variables required by B. babyrussa species including NDVI, barren soil, elevation, and river network. The particular location was a Batabual landscape sizing 292.60 km2 located in the east parts of Buru island. Based on NDVI, less vegetation covers were observed in north and east parts of Batabual. In contrast, NDVI values were higher in the central, west, and south indicating that half of the landscape was covered by intact primary forest. Batabual has a hilly landscape surrounded by coastal areas with hilly areas were observed in the south and west. There were 2 river streams in the east parts. The analysis has divided the landscape into several parts based on the habitat suitability levels. About one third of the landscape located in north was considered less and not suitable for Babirusa. Some areas in west were also considered moderate to be inhabited by Babirusa considering a presence of hilly landscape that may limit the vertical distribution of Babirusa. Most suitable habitats were estimated in central parts of the landscape spanning to the south. South parts of the landscape were characterized by high NDVI values and forest covers then these areas were considered as suitable habitats for Babirusa. The size of this suitable habitat was estimated around 188.62 km2 or more than half of the size (64.46%) of Batabual landscape.

ecology↗

bioRxiv2021

Modeling The Effect of Forest Fire and Deforestation on Mid-Sized Wild Cat (Felids) Occupancy in SE Asian Tropical Rainforest

Felids are mammal groups that also experiencing the effects of forest fire and deforestation rate. By using camera detection method, two felid species, Prionailurus bengalensis and Pardofelis marmorata, of tropical rainforests in SE Asia have been studied. The studied area was a rainforest in Sumatra that has experienced several forest fires with annual deforestation rates of 1.69%-2.89%. Occupancy model using Akaike Information Criterion (AIC) is in agreement that deforestation rate is the best explanatory covariate explaining the declining occupancy of those felid species. P. marmorata was known more sensitive to the both deforestation rate and forest fire frequency covariate effects since it has similar AIC values. While P. bengalensis was slightly affected by forest fires. Values of Area Under The Curve (AUC) of Receiver Operating Characteristic (ROC) were > 0.5 and these indicate adequate probability of forest fire effects on felid occupancy. Cut off value of occupancy of P. bengalensis was higher than P. marmorata. For P. bengalensis, the cut off value was 1.75 leading to a sensitivity and specificity of 62%. This is the threshold value for the prediction of numbers of P. bengalensis individual occurred where both sensitivity and specificity are maximized and as an effect of forest fire, and this can be used to classify areas as occupied by P. bengalensis.

ecology↗

bioRxiv2021

Spatial modeling of tidal and land use impacts on Escherichia coli contamination and fluctuation in Asia's urban river environmental gradient

In the river, pathogens are the leading cause for rivers to exceed water and health quality standards. The GIS based spatial modeling and analysis were conducted to estimate Escherichia coli (E. coli) contaminated river bodies based on environmental and spatial gradients such as dissolved oxygen, pH, tidal, temperature and current in Asias urban river located in Kapuas river of Kalimantan. The E. coli was sampled from the river mouth up to the upstream land uses dominated by residential. The E. coli contamination was higher in the river mouth and in residential area as well. Likewise, E. coli contamination was higher during the low tide than high tide. During the high tide, the E. coli contamination were significantly affected by temperature and current (r2>0.5). Meanwhile, during the low tide, there were no dominant environmental factors that affect E. coli contamination. Hence, by knowing the spatial model of E. coli contamination driven by tidal, land use and environmental gradients, this paper has contributed to the advance management of water and river system.

ecology↗

bioRxiv2021

Modeling microbial diversity across different soil ecosystems and environmental covariate selections in tropical SE Asian landscape

Microbes play essential roles in the ecology of various environments and structure. Diversity of soil microbial communities is an important scientific interest in tropical landscape including in South East Asia. Soil environment in SE Asia is diverse and this influences the microbial diversity. Soil microbes in this study were collected using DNA isolation protocols and the whole microbial community structure of sampled soil was analyzed through next generation sequencing. Soil microbial identification was conducted by amplifying the 16S rRNA gene. Soils were sampled from 4 different environments in Sumatra and Kalimantan ecosystems representing plantation, swamp, peatland, and coastal ecosystems. Measured soil covariates including soil organic carbon C analyzed based on the Walkley-Black method and Kjeldahl method for N. Model of microbes in soil ecosystems were based on Akaike model selection (AIC) by testing the influence of soil covariates on soil microbial phylum. The microbial community was found to be comprising of a total number of 11 phyla. In soil of coastal ecosystem, microbial diversity at phylum level were dominated by Proteobacteria (82.3%), Actinobacteria (9.41%), Acidobacteria (4.7%), and the lowest was Bacteroidetes and Chloroflexi (0.58%). In plantation soil, the microbial abundance order was Firmicutes (41.6%) > Actinobacteria (29.7%) > Acidobacteria (20.0%) > Gemmatimonadetes (5.94%). The soil microbial abundance order in swamp was Proteobacteria (42.2%) > Acidobacteria (20.04%) > Bacteroidetes > (10.46%) > Actinobacteria (9.24%). In soil of peatland ecosystem, taxonomic assignments of microbial at the phylum level were dominated by Firmicutes (66.18%), Proteobacteria(16.94%), and Actinobacteria (16.87%). According to the values of AIC, Firmicutes was a microbial phylum that has high abundance in soil ecosystems influenced by pH covariates with AIC values of -6.54. Other soil covariates show less influence on Firmicutes with AIC values of -5.06. The combination model also show that pH cofactor was the important determinants with AIC values of -0.54 for Firmicutes (pH+C) and Firmicutes (pH+N) models. While AIC value for combination model of Firmicutes (C+N) only equals to 0.14.

ecology↗

bioRxiv2021

Hydrosphere occupancy modeling ({psi}) and Akaike (AIC) habitat model selection of urban amphibian in West Java landscape

Amphibians are animal that requires combinations of hydrosphere (riparian vegetation, water body) and vegetation (trees) microhabitats. In urban settings, those microhabitats are scarce and disappearing. One of areas that still have sufficient microhabitats to support amphibian populations is located in an 88.9 Ha urban forests of Universitas Indonesia Campus in West Java. Here, this paper aims to assess and model the several amphibian species occupancy ({Psi}) with vegetation covers, riparian vegetation, and water bodies based on Akaike habitat selection (AIC) indices. The studied amphibian species include Bufo melanosticus, Hylarana nicobariensis, Fejervarya limnocharis, and Polypedates leucomystax. For modeling, 7 microhabitat models were developed and tested for amphibian species occupancy with covariates including vegetation cover, riparian vegetation, and water body microhabitats. The Principle Component Analysis (PCA) shows that the occupancies of amphibian were influenced mostly by the presences of water bodies followed by riparian vegetation, and vegetation covers. According to the values of {Psi} and AIC, Polypedates leucomystax and Fejervarya limnocharis were species that have high occupancy in riparian vegetation microhabitats with {Psi} values of -14.18 and -12.59. Likewise, Hylarana nicobariensis has an equal occupancy in vegetation, riparian vegetation, and water body microhabitats. While Bufo melanosticus shows high occupancy in vegetated microhabitats ({Psi} = -14.18) rather than in riparian vegetation and water bodies ({Psi} = -8.79). The combinations of riparian vegetation and water bodies show higher occupancy ({Psi} = -8.00) rather than {Psi}(vegetation cover+water body = -5.64) and {Psi}(vegetation cover+ riparian vegetation = -4.36) combinations.

ecology↗

bioRxiv2021

Anopheles spp. distribution and climatological niche modeling to predict malaria potential along bioclimatic envelope gradients in South Coast of West Java landscape

Malaria remains a major public health problem mainly in particular South East Asian countries. As malaria transmission and Anopheles spp. continues to spread, control interventions should emphasize on the ability to define potential areas that can favor Anopheles spp. distribution. Then there is an urgent need to use novel approach capable to predict potential spatial patterns of Anopheles spp. and delineate malaria potential hotspots for better environmental health planning and management. Here, this study modeled Anopheles spp. potential distribution as a function of 15 bioclimatic variables using Species Distribution Modeling (SDM) in South Coast of West Java Province spans over 20 km from West to East. Findings of this study show that bioclimatic variables and SDM can be used to predict Anopheles spp. habitat suitability, suggesting the possibility of developing models for malaria early warning based on habitat suitability model. The resulting model shows that the potential distributions of Anopheles spp. encompassed areas from West to Central parts of the coasts, with Central parts were the most potential prevalence areas of Anopheles spp. considering this area has higher precipitation. The less potential prevalence areas of Anopheles spp. were observed in the East parts of the coast. The model also shows that inland areas adjacent to the settlements were more potential in comparison to the areas near coast and in the beach. Land cover conditions dominated by cropland, herbaceous wetland, and inundated land were also influencing the Anopheles spp. potential distribution.

ecology↗

bioRxiv2021

Phylogeography and Proline amino acid usage of Asian tiger mosquito Aedes albopictus (Skuse 1894) populations along landscape gradients in Indonesia

Asian tiger mosquito Aedes albopictus (Skuse 1894) is one of mosquito-borne vector that globally distributed including Southeast Asia. Despite its wide distributions, information on phylogeography and its determinant factors influencing A. albopictus genetic diversity and speciation is still lacking, mainly in SE Asia country. Considering this, the phylogeography of A. albopictus along with its genetic attributes in Indonesia has been assessed. The results identify that there are 2 distinct clades of A. albopictus phylogeography. First clade was related to the human-mediated dissemination. Relative Synonymous Codon Usage (RSCU) shows the TTG, CTG, GTG, ACG, GCG, and GGG codons were seldom represented. While GGA, CGA, and followed by TAT, CAT, CCT, TCT, AAC, and TTC codons were common. From a total of 60 codons, 40% codon has RSCU > 1and 21.6 % has RSCU < 1. The differences between west and east part populations can be observed in proline amino acid signaled by CCT and CCC codons. In this amino acid, east A. albopictus has higher CCC than CCT codons. Since proline is functioned to provide energy for flight, then the differences of this proline related codon among A. albopictus populations were related to the landscape variations in west and east parts of Indonesia with east parts have more rugged landscape and this condition is quite demanding for aerial animal distribution since it requires more flight energy.

ecology↗

bioRxiv2021

Phylogeography, codon usage, and DNA barcoding of lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) populations in Indonesia

Fruit bat (Pteropodidae) is one of the mammals that is common in environments and widely distributed from subtropical to tropical Asia. Whereas the information on phylogeography of fruit bat Cynopterus brachyotis is still limited. From this situation, this paper aims to assess the phylogeography, codon usage, and DNA barcoding of C. brachyotis populations in Indonesia. Phylogeography was developed based on 657 bp of the mtDNA COI gene for all bat individuals and Bayesian inference to construct the phylogeny tree. The C. brachyotis populations in Indonesia are different to the populations from the Asias continent. The results show that C. brachyotis populations in Indonesia were divided into 3 distinct clades. A putative geographical barrier, recent, and rapid range expansion in the Sunda lineage associated with changes in sea levels, possibly coupled with related ecological differences, may have driven population divergence, allopatric, and sympatric speciation. Codon usage and high frequency were also contributing to the dispersal of C. brachyotis forming a distinct population.

ecology↗

bioRxiv2021

Underlying environmental factors and geomagnetic fields linked to 45 pilot whales Globicephala macrorhynchus stranding in Modung white beach, Indonesian coast on 19th February 2021

The reason whale and dolphin stranding is not fully understood and it is not linked to a standalone variable. Theories assume intertwined factors including sickness, underwater noise, navigational error, geographical features, the presence of predators, poisoning from pollution or algal blooms, geomagnetic field, and extreme weather are responsible to whale stranding. On 19th February 2021, a pod consists of 45 pilot whales Globicephala macrorhynchus was stranded in a remote 7050 m2 Modung white beach of Indonesian coast. This paper aims to assess the environmental factors that may be can explain and link to this stranding cases. Those factors include bathymetry, plankton cell density measured using MODIS, water sediment load measured using Sentinel 2 Bands 4,3,1, vessel traffic, precipitation (inch) and thunder (CAPE index J/kg), water salinity and temperature, and geomagnetic field (nT). The results show the water near stranding sites were shallow, has sediment load, high plankton density, warmer, receiving torrential rain prior stranding, having weak geomagnetic field and high total magnetic field change/year. The combination of those environmental covariates may influence the behavior, navigation, and echolocation of the said stranded pilot whale.

ecology↗

bioRxiv2021

Modeling land use impacts on spatial distribution of floating plastic litter in surface water of Southeast Asian archipelago

Plastics are present in many ecosystems including floating in surface water of remote archipelago and this can lead to the increase in plastic litter density. Whereas the spatial model of plastic litter density related to the population inhabits isolated archipelago is still limited. And what are the underlying factors driving the presence of plastic litter is also poorly understood. This study is trying to find the answers of those questions. The study was implemented in Thousand Island archipelago located in North of Java Island, one of populated islands in Southeast Asia. The studied surface water covers an area of 10000 Ha and consists of 10 islands with 3 islands are occupied by settlements and the remaining islands are occupied by vegetation. This study has recorded 3 types of floating macro-litter from water that consist of PET, HDPE, and LDPE litter. The plastic litter was observed concentrated in the east sides of archipelago where the populated islands were located. The spatial models show LDPE litter was distributed in the vast areas in comparison to PET and HDPE litter. Beside land use variables, the model has confirmed that the population density was the main underlying factors contribute to the plastic litter density in Thousand Island archipelago. The model can be applied to estimate PET (AIC = -0.53060) and HDPE (AIC = 18.28828) litter density. While LDPE litter density was influenced by population (AIC = 22.60201) rather than population density factors.

ecology↗

bioRxiv2021

Spatial model of water quality in Southeast Asian urban lake based on HBI using macrozoobenthos diversity as a proxy

Urban lake is one of ecosystem that has experienced anthropogenic pressures and this can affect its water quality. One of a robust approach to assess the water quality is by using Hilsenhoff Biotic Index (HBI). This tool is quite versatile since it can be applied by using any aquatic organism as proxy including macrozoobenthos. This invertebrate group also has an advantage since it is common and easy to collect. Here this study is first, aiming to provide HBI based water quality spatial model using macrozoobenthos as a proxy applied in urban lake in West Java in Southeast Asia and second to seek the best model that can represent the water quality variables in particular dissolved oxygen (DO), pH, and temperature. Based on the spatial model and HBI, either inlet or outlet parts of the lake, it has better water quality in comparison to central parts. Based on HBI values, water quality in inlet and outlet parts (HBI = 6.7) is categorized as fair and poor (HBI = 6.9) for the central parts of the lake. The increase in HBI and decrease in water quality are positively correlated with the increase in water temperature variable in comparison to water DO and pH variables. Akaike model selection confirms that the macrozoobenthos diversity can be used as a proxy for increase in water temperature ({Psi})HBI (~temp)(AIC = -10.264) followed by combination of water temperature increase and decrease in DO({Psi})HBI (~temp+DO)(AIC = -9.042398).

ecology↗

bioRxiv2021

Aerosphere occupancy ({psi}) model of lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) related to tree species in Asia mountainous paddy fields

Bat is animal that occupies aerosphere, especially fruit bats that forage on the space around the trees. The fruit bats use whether narrow space below tree canopy or in edge space on the edge of canopy. Whereas the aerosphere occupancy of fruits bats related to the specific tree species is poorly understood. Here, this paper aims to assess and model the association of fruit bat Cynopterus brachyotis aerosphere occupancy ({Psi}) with tree species planted in mountainous paddy fields in West Java. The studied tree species including Alianthus altissima, Acacia sp., Cocos nucifera, Mangifera indica, Pinus sp., and Swietenia macrophylla. The result shows that the tree species diversity has significantly (x2= 27.67, P < 0.05) affected the C. brachyotis aerosphere occupancy. According to values of {Psi} and occupancy percentage, high occupancy of narrow space by C. brachyotis was observed in Swietenia macrophylla ({Psi} = 0.934, 78%), followed by Alianthus altissima ({Psi} = 0.803, 57%), and Mangifera indica ({Psi} = 913, 55%). While high occupancy of edge space was observed in Mangifera indica ({Psi} = 0.685, 41%), followed by Pinus sp. ({Psi} = 0.674, 38%), and Alianthus altissima sp. ({Psi} = 0.627, 36%). The best model for explaining C. brachyotis occupation in narrow space is the tree height with preferences on high tree ({Psi}~tree height, AIC = 1.574, R2= 0.5535, Adj. R = 0.4047). While for edge space occupant, the best model is also the tree height ({Psi}~tree height, AIC = -26.1510, R2= 0.7944, Adj. R = 0.7258).

ecology↗

bioRxiv2021

Akaike model selections of the vegetation structures and aerosphere factors in supporting lesser short nosed fruit bat (Cynopterus brachyotis Muller, 1838) populations in Asia mountainous paddy fields

As an aerial and arboreal fauna, the abundances and populations of fruit bat Cynopterus brachyotis were influenced by the vegetation structures and aerosphere condition variables of fruit bat ecosystems. While mountaineous paddy field is an unique habitat since the trees are scarce and has exposure to the aerosphere variables including air temperature and humidity. Here this paper aims to select the best vegetation structures and aerosphere factors that support the abundance of C. brachyotis in mountainous paddy field landscape in West Java. The model selection was using AIC methodology by testing 15 models including 5 single models and 10 combination models of explanatory variables. Based on the model, tree height and combinations of tree height and elevation produced the best prediction for the bat abundances, as described by low values of AIC and the highest values of R2 and adjusted R2. For the best models, the AIC values ranged from 16.674 to 17.603, from 0.3404 to 0.4144 (R2), and 0.2461 to 0.2192 for adjusted R2. Regarding conservation of C. brachyotis and learning from the model, the conservation approaches mainly in mountainous paddy fields are encouraged to protect and conserve high altitude landscapes and trees with height > 10 m. Whereas the AIC results show lack of aerosphere variable effects on C. brachyotis (AIC: 19.346-20.406, R2: 0.1124-0.001353, and adjusted R2: -0.01444 - -0.1413).

ecology↗