Gono Semiadi

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

BackgroundElucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.ResultsOur data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.ConclusionsOur results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.

Declining populations of the Javan warty pig Sus verrucosus

We conducted an interview-based survey for the Javan warty pig Sus verrucosus, endemic to the islands of Java and Bawean in Indonesia. The species occurs in 10 isolated areas, although some additional, probably very small populations, may remain. Compared to a survey conducted in 1982, 17 of the 32 (53%) populations are extinct or have dropped to levels so low that local hunters have failed to encounter the species in recent years. This indicates a rapid population decline. We hypothesize that this loss is primarily caused by a decline in suitable habitat, especially stands of teak Tectona grandis forest or similar forest plantations, and by high hunting pressure. Competition from and hybridization with the Eurasian wild boar Sus scrofa may be further threats to S. verrucosus. Rapid action is needed to prevent extinction in the wild. We recommend effective pro- tection of selected S. verrucosus populations, lobbying of the Government to give protected status to S. verru- cosus, conducting ecological research and investigating crop damage issues, and establishment of conservation breeding programmes.

Endogenous Gibbon Ape Leukemia Virus Identified in a Rodent (Melomys burtoni subsp.) from Wallacea (Indonesia)

ABSTRACT Gibbon ape leukemia virus (GALV) and koala retrovirus (KoRV) most likely originated from a cross-species transmission of an ancestral retrovirus into koalas and gibbons via one or more intermediate as-yet-unknown hosts. A virus highly similar to GALV has been identified in an Australian native rodent (Melomys burtoni) after extensive screening of Australian wildlife. GALV-like viruses have also been discovered in several Southeast Asian species, although screening has not been extensive and viruses discovered to date are only distantly related to GALV. We therefore screened 26 Southeast Asian rodent species for KoRV- and GALV-like sequences, using hybridization capture and high-throughput sequencing, in the attempt to identify potential GALV and KoRV hosts. Only the individuals belonging to a newly discovered subspecies of Melomys burtoni from Indonesia were positive, yielding an endogenous provirus very closely related to a strain of GALV. The sequence of the critical receptor domain for GALV infection in the Indonesian M. burtoni subsp. was consistent with the susceptibility of the species to GALV infection. The second record of a GALV in M. burtoni provides further evidence that M. burtoni, and potentially other lineages within the widespread subfamily Murinae, may play a role in the spread of GALV-like viruses. The discovery of a GALV in the most western part of the Australo-Papuan distribution of M. burtoni, specifically in a transitional zone between Asia and Australia (Wallacea), may be relevant to the cross-species transmission to gibbons in Southeast Asia and broadens the known distribution of GALVs in wild rodents. IMPORTANCE Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts neither are closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host whose range overlaps those of both gibbons and koalas. Using hybridization capture and high-throughput sequencing, we have screened a wide range of rodent candidate hosts from Southeast Asia for KoRV- and GALV-like sequences. Only a Melomys burtoni subspecies from Wallacea (Indonesia) was positive for GALV. We report the genome sequence of this newly identified GALV, the critical domain for infection of its potential cellular receptor, and its phylogenetic relationships with the other previously characterized GALVs. We hypothesize that Melomys burtoni, and potentially related lineages with an Australo-Papuan distribution, may have played a key role in cross-species transmission to other taxa.

Genome-wide SNP data unveils the globalization of domesticated pigs

AbstractBackgroundPigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.ResultsA deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.ConclusionsKey events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

New record of Melomys burtoni (Mammalia, Rodentia, Murinae) from Halmahera (North Moluccas, Indonesia): a review of Moluccan Melomys

Abstract Mosaic-tailed rodents of the genus Melomys belong to the Australasian old endemic murine radiation and exhibit a rat-like morphology with arboreal or scansorial specializations. Here we report a new population of Melomys burtoni from the island of Halmahera (in the North Moluccas, Indonesia). Our molecular phylogenetic results highlight close relationships and recent evolutionary divergences among M. burtoni from Halmahera and the Australo-Papuan taxa M. burtoni and M. lutillus and other Moluccan taxa, including M. paveli. Multivariate as well as geometric morphometric analyses of cranial, and dental features support the recognition of M. burtoni from Halmahera as a slightly distinctive insular population, preventing us from elevating it as a new taxa. This population is recorded from lowland secondary forest and forest edge habitats in south-central Halmahera. As with other Moluccan endemic murines, colonization by an Australo-Papuan ancestor and subsequent isolation is the probable mode of diversification for M. burtoni in Halmahera. The discovery of Melomys in Halmahera fills a previously puzzling gap in knowledge of the murine fauna of the Moluccas and the biogeography of the Wallacean region.

Gambaran Darah Kukang Dipelihara pada Kandang Penangkaran

Maintenance of wildlife outside its original habitat is usually for the purposes of the exhibition in zoos, for research and captive breeding effort, especially for endangered species which eventually return to nature. The adaptability of the animals outside their original habitat can be seen from their health and their ability to reproduce in ex situ (captive) environment. One of the parameter that can be used to determine a health an animal is by observing their blood parameters and compared it with normal reference, however for many wild animals reference data for normal blood parameters are limited or not available. This study was conducted to determine a normal reference of blood parameters of slow lories that are kept in captive breeding condition, consisted of routine hematology and blood chemistry. This study used five animals consisting of four of N. coucang (1 male and three female) and one female N. javanicus. The results of the analysis showed that the value of hemoglobin, MCV, PDW, MPC, and erythrocytes (RBC) were higher on the male slow lories, while leukocytes (WBC), hematocrit, and MCHC were higher on the female. There were no significant differences between blood parameters of N. coucang and N. javanicus .

Conservation genomics reveals possible illegal trade routes and admixture across pangolin lineages in Southeast Asia

The use of genome-wide genetic markers is an emerging approach for informing evidence-based management decisions for highly threatened species. Pangolins are the most heavily trafficked mammals across illegal wildlife trade globally, but critically endangered Sunda pangolins (Manis javanica) have not been widely studied in insular Southeast Asia. We used > 12,000 single nucleotide polymorphic markers (SNPs) to assign pangolin seizures from illegal trade of unknown origin to possible geographic sources via genetic clustering with pangolins of known origin. Our SNPs reveal three previously unrecognized genetic lineages of Sunda pangolins, possibly from Borneo, Java and Singapore/Sumatra. The seizure assignments suggest the majority of pangolins were traded from Borneo to Java. Using mitochondrial markers did not provide the same resolution of pangolin lineages, and to explore if admixture might explain these differences, we applied sophisticated tests of introgression using > 2000 SNPs to investigate secondary gene flow between each of the three Sunda pangolin lineages. It is possible the admixture which we discovered is due to human-mediated movements of pangolins. Our findings impact a range of conservation actions, including tracing patterns of trade, repatriation of rescue animals, and conservation breeding. In order to conserve genetic diversity, we suggest that, pending further research, each pangolin lineage should as a precaution be protected and managed as an evolutionarily distinct conservation unit.

Gambaran Umum Kajian Profil Hormon Steroid Menggunakan Metode Non-Invasif dari Sampel Feses

Kajian terhadap profil hormon-hormon steroid merupakan kunci penting dalam upaya memahami aspek fisiologis satwa. Beberapa dekade terakhir telah dikembangkan metode alternatif untuk mengetahui profil hormon steroid, yaitu melalui pengukuran metabolit hormon steroid yang diekskresikan melalui ekskreta tubuh seperti feses. Metode tersebut dikenal sebagai metode non-invasif. Metode ini memungkinkan pengumpulan sampel secara terus menerus dalam jangka panjang dengan meminimalisasi gangguan terutama pada satwa liar. Kajian terhadap profil metabolit hormon steroid yang terukur dapat diaplikasikan antara lain untuk mengetahui status reproduksi, penentuan jenis kelamin, studi perilaku hingga monitoring tingkat stres satwa. Berbagai kajian dengan memanfaatkan metabolit hormon steroid telah berhasil diaplikasikan pada berbagai taksa vertebrata. Tulisan ini memberikan gambaran terkini mengenai aplikasi metode non-invasif untuk kajian profil metabolit hormon steroid dari sampel feses.

Karakteristik Karkas, Sifat Fisik dan Kimia Daging Rusa Sambar (Rusa unicolor)

Local variety is the major component in upland rice cultivation as well as breeding material in variety improve-ment. Local upland rice varieties have been adapted to specific location, preferred and adopted by farmers although they are late in maturity. These reasons make it majority of farmers in West Pasaman District (West Sumatra) still cultivate local upland rice varieties. To know the yield potential and agronomic characters of widely cultivated of upland rice in West Pasaman District, a variety trial conducted in 2010. Five local varieties and one improve variety planted a Randomized complete block arrangement with three replications. Observa-tion conducted on agronomic characters and yield and yield components. The results showed that local variteies were tall (153-171 cm) and late maturity (130-157 days). The local varieties also showed higher number of spikelet/panicle (249-454) lighter 1.000 grains weight (<20 g) and higher yield than improved variety (4.27-5.51 compared to 2.85 t/ha). In general all plant characters showed high heritability estimate (except number of productive tiller/hillr). High estimated of genetic variation coefficient and genetic advance were shown on number of grain per panicle. Based on these genetic parameters, selection at early generation for high yield can conducted on number of grain per panicle.Phosporus (P) deficiency is one of limiting factor for rice growth. In Indonesia P deficiency much occurs in acid soils. The use of P deficiency tolerant varieties is the best solution compared to the application of P fertilizer due to more efficient in cost. The purpose of this study was to evaluate the local rice germplasm collected from several regions in Indonesia to P deficiency in acid soil. The study was conducted in Jasinga West Java during wet season of 2006- 2007 with the soil condition lack of P. The experiments were conducted with the two treatments: first, without P fertilizer and second with P fertilizer equivalent of 25 kg P/ha. The total 100 accessions of rice germplasm were screened in this field based on a randomized block design with three replications. Fertilizing were given on experiments I and II with the composition: urea 300 kg/ha and 100 kg KCl. The field design was done by plotting size is 1 x 5 m2, spacing plant of 25 cm x 25 cm, and planting two seeds per hole. The yield components characters which were observed: number of tillers, plant dry weight, plant height and flowering. The results of combined analysis showed that there is a significant interaction between P and genotype on the tiller number, whereas the dry weight of plant, plant height, and flowering were is not significant. The evaluation of 100 local rice genotypes to P deficiency by indicators of the tiller number and dry weight of plants obtained 19 genotypes that are tolerant to P deficiency with the relative value of tillers number and dry weight of plants more than 80%. Local varieties Mandalet, Ganefo, Padi Belanda, Pulut Jangan, Padi Ubek Bala, and Padi Krayan were the most tolerant to conditions without P which showed the tillers number more 1-21% rather than the conditions with P fertilizer. There are three selected genotypes, Pulut Jangan, Padi Ubek Bala, and Padi Krayan which increased the number of tillers and dry weight of plants in without P conditions. The increasing of tillers number were reach 1-17% while the dry weight increased 12-41%.

Karakteristik genetik pada famili cervidae (Cervus unicolor, Cervus timorensis, dan Axis kuhlii) berdasarkan 12SrRNA mtDNA

Genetic analysis from three species of Indonesia Cervidae (sambar deer, Cervus unicolor; rusa deer, Cervus timorensis; and Bawean deer, Axis kuhlii) was conducted to analyze their relationship. Tissues and blood from twelve sambar deer, one rusa deer and three Bawean deer were collected and analyzed for 12SrRNA using Primer forward (L1091) and reverse (H1478). The results indicated the amplication of mtDNA were 389 base nucleotide. There were 22 polimorphic sites, which were dominated by transition and gave 9 haplotypes that were 5 in sambar deer, 1 in rusa deer and 3 in Bawean deer.