Achmad Farajallah

Consequences of tropical land use for multitrophic biodiversity and ecosystem functioning

Our knowledge about land-use impacts on biodiversity and ecosystem functioning is mostly limited to single trophic levels, leaving us uncertain about whole-community biodiversity-ecosystem functioning relationships. We analyse consequences of the globally important land-use transformation from tropical forests to oil palm plantations. Species diversity, density and biomass of invertebrate communities suffer at least 45% decreases from rainforest to oil palm. Combining metabolic and food-web theory, we calculate annual energy fluxes to model impacts of land-use intensification on multitrophic ecosystem functioning. We demonstrate a 51% reduction in energy fluxes from forest to oil palm communities. Species loss clearly explains variation in energy fluxes; however, this relationship depends on land-use systems and functional feeding guilds, whereby predators are the most heavily affected. Biodiversity decline from forest to oil palm is thus accompanied by even stronger reductions in functionality, threatening to severely limit the functional resilience of communities to cope with future global changes.

Variations in long- and middle-wavelength-sensitive opsin gene loci in crab-eating monkeys

We analyzed variations in long (L)- and middle (M)-wavelength-sensitive opsin gene loci in crab-eating monkeys. Unlike humans, most monkeys have a single L and a single M gene. Two variant genotypes, one with only one opsin gene (dichromatic) and one with tandemly arrayed multiple genes, were also found in the monkeys. However, the frequency of the former was 0.47%, and that of the latter was 5% in the monkeys, while 2% and 66%, respectively, in Caucasian males. The two variants were found only in Java Island, Indonesia, and South Thailand, respectively. The data suggest that the frequency of each genotype is different among Old World primates.

Electroretinogram analysis of relative spectral sensitivity in genetically identified dichromatic macaques

The retinas of macaque monkeys usually contain three types of photopigment, providing them with trichromatic color vision homologous to that of humans. However, we recently used molecular genetic analysis to identify several macaques with a dichromatic genotype. The affected X chromosome of these animals contains a hybrid gene of long-wavelength-sensitive (L) and middle-wavelength-sensitive (M) photopigments instead of separate genes encoding L and M photopigments. The product of the hybrid gene exhibits a spectral sensitivity close to that of M photopigment; consequently, male monkeys carrying the hybrid gene are genetic protanopes, effectively lacking L photopigment. In the present study, we assessed retinal expression of L photopigment in monkeys carrying the hybrid gene. The relative sensitivities to middle-wavelength (green) and long-wavelength (red) light were measured by electroretinogram flicker photometry. We found the sensitivity to red light to be extremely low in protanopic male monkeys compared with monkeys with the normal genotype. In female heterozygotes, sensitivity to red light was intermediate between the genetic protanopes and normal monkeys. Decreased sensitivity to long wavelengths was thus consistent with genetic loss of L photopigment.

Decreasing Stoichiometric Resource Quality Drives Compensatory Feeding across Trophic Levels in Tropical Litter Invertebrate Communities

Living organisms are constrained by both resource quantity and quality. Ecological stoichiometry offers important insights into how the elemental composition of resources affects their consumers. If resource quality decreases, consumers can respond by shifting their body stoichiometry, avoiding low-quality resources, or up-regulating feeding rates to maintain the supply of required elements while excreting excess carbon (i.e., compensatory feeding). We analyzed multitrophic consumer body stoichiometry, biomass, and feeding rates along a resource-quality gradient in the litter of tropical forest and rubber and oil-palm plantations. Specifically, we calculated macroinvertebrate feeding rates based on consumer metabolic demand and assimilation efficiency. Using linear mixed effects models, we assessed resource-quality effects on macroinvertebrate detritivore and predator communities. We did not detect shifts in consumer body stoichiometry or decreases in consumer biomass in response to declining resource quality, as indicated by increasing carbon-to-nitrogen ratios. However, across trophic levels, we found a strong indication of decreasing resource quality leading to increased consumer feeding rates through altered assimilation efficiency and community body size structure. Our study reveals the influence of resource quality on multitrophic consumer feeding rates and suggests compensatory feeding to be more common across consumer trophic levels than was formerly known.

Reproductive Biology of Ovigerous Female Emerita emeritus (Crustacea, Decapoda) in Bengkulu Coastal Waters, Indonesia: Egg Production and Reproductive Output

Abstract Emerita emeritus is an abundant species in Bengkulu coastal waters, but the knowledge of its reproductive biology is poor. The present study was conducted to elucidate the reproductive aspects of ovigerous female E. emeritus, including fecundity, egg volume and reproductive output. This study was conducted between January 2015 and January 2016 in Bengkulu coastal waters, Indonesia. Samples were collected manually using shovels and hands. The results showed that ovigerous females occurred every month. Fecundity increased significantly in ovigerous females proportional to the size. No correlation was shown between sea surface temperature and egg production. Fecundity and reproductive output decreased throughout the embryonic development.

First record of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) from south of Java, Indonesia

Abstract Background Three specimens of Puerulus mesodontus Chan, Ma & Chu, 2013 (Crustacea, Decapoda, Achelata, Palinuridae) were collected from Palabuhanratu Bay, southern Java, Indonesia. There is no previous record on the presence of the species in Indonesia. This finding represents the first record of this species in Java, Indonesia, and confirms that the species is present in the Indian Ocean. The morphological characters of the species are described. New information This paper contains a new distribution record of a lobster species from Indonesian waters.

A New Megophrys Kuhl and Van Hasselt (Amphibia: Megophryidae) from southwestern Sumatra, Indonesia

Megophrys lancip sp. nov., from the Bukit Barisan mountain range of southwestern Sumatra, Indonesia, is described on the basis of molecular and morphological evidence. The new species is distinguished from its congeners in Sumatra, Java, Borneo, and the Philippines by having a medium-sized body, snout with an extremely pointed rostral appendage, a medium-sized triangular eyelid appendage, a dorsolateral fold extending from just behind the eye to the groin, vomerine teeth, vocal slits, nuptial pads on the dorsomedial surface of the first and second fingers in males, and in lacking a Y, X, or H-shaped fold on the dorsum. Morphologically, the new species is most similar to M. montana, but it has a longer rostral appendage, shorter eyelid appendages, and less developed toe webbing. We also evaluate the taxonomic status of M. parallela and comment on the occurrence of M. aceras in Sumatra.

Sex-changing patterns of Akoya pearl oyster (Pinctada fucata)

BackgroundPearl production by transplantation in Akoya pearl oyster (Pinctada fucata) is a biotechnology developed in Japan that skillfully utilizes the pearl-forming ability of oysters. In this method, cultured pearls are formed from a pearl nucleus and a small piece of mantle transplanted into the gonads of recipient pearl oysters. In this study, we hypothesized that the sex of the recipient pearl oyster might affect the quality of pearl produced. While some previous studies have examined the sex of Akoya pearl oyster, detailed information is lacking.ResultsTo investigate sex in Akoya pearl oyster, we collected small gonadal fragments from 1-year-old pearl oysters by biopsy. Using the collected gonad fragment, the sex of the oysters was determined by microscopic observation, and the remaining samples were stored for gene expression analyses. All oysters were labeled to distinguish each individual for serial samplings every four months over the 2-year study period. At the start of experiment, nearly all of the pearl oysters were male, but the male:female ratio ofmale decreased over the course of the experiment. Interestingly, the number of males increased after spring, during the breeding season. This suggests that, in pearl oyster, sex is affected by season. Expression analysis of sex-related genes (Dmrt2, Vtg, Zp) indicated that all genes were expressed in all individuals and all periods.ConclusionsThese results suggest that Akoya pearl oysters are hermaphroditic, and that females appear as necessary, such as during the breeding season. These findings could contribute to higher efficiency and quality of pearl cultivation.

Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis

Abstract The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.

Efektivitas Ivermectin dan Albendazole dalam Melawan Ostertagia pada Anakan Domba di Bogor, Indonesia

Giving a half-dose of an anthelmintic is a simple method for detecting resistance in parasites infesting small ruminants. When a single anthelmintic fails in native sheep from Indonesia, a combination of anthelmintics from different chemical classes with different mechanism of action is an alternative parasite-control strategy. This study compared the anthelmintic effectiveness of ivermectin (IVM) and albendazole (ABZ) have given either separately as a full-dose or half-dose or co-administered to sheep naturally infected with Ostertagia. Twelve sheep from Bogor, Indonesia were divided into six groups based on the anthelmintic treatment: half-dose IVM, full-dose IVM, half-dose ABZ, full-dose ABZ, combined (half-dose IVM + half-dose ABZ), and control groups. The treatment effectiveness was determined using the Faecal egg count reduction (FECR) on before and after 7, 14, 21, 28, 35, and 42 days of treatment. FECR of half-dose IVM, full-dose IVM, half-dose ABZ, full-dose ABZ, and both combined ranged from 78100, 96100, -7189, -52164, and 54100, respectively. The results showed that full-dose IVM was the most effective to against Ostertagia until 42 days and followed the combined that effective until 28 days. Half-dose and full-dose ABZ weren’t effective to against Ostertagia.