Like Chinese Silkie, Indonesian Ayam Cemani exhibits fibromelanosis or dermal hyperpigmentation and possesses complex segmental duplications on chromosome 20 that involve the endothelin 3 gene, EDN3. A genomic region, DR1 of 127 kb, together with another region, DR2 of 171 kb, was duplicated by unequal crossing over, accompanied by inversion of one DR2. Quantitative PCR and copy number variation analyses on the Cemani genome sequence confirmed the duplication of EDN3. These genetic arrangements are identical in Cemani and Silkie, indicating a single origin of the genetic cause of Fm. The two DR1s harbor two distinct EDN3 haplotypes in a form of permanent heterozygosity, although they remain allelic in the ancestral Red Jungle Fowl population and some domesticated chicken breeds, with their allelic divergence time being as recent as 0.3 million years ago. In Cemani and Silkie breeds, artificial selection favoring the Fm phenotype has left an unambiguous record for selective sweep that extends in both directions from tandemly duplicated EDN3 loci. This highly homozygous tract is different in length between Cemani and Silkie, reflecting their distinct breeding histories. It is estimated that the Fm phenotype came into existence at least 6600–9100 years ago, prior to domestication of Cemani and Silkie, and that throughout domestication there has been intense artificial selection with strength s > 50% in each breed.

The colonization of Madagascar by Austronesian-speaking people during AD 50–500 represents the most westerly point of the greatest diaspora in prehistory. A range of economically important plants and animals may have accompanied the Austronesians. Domestic chickens ( Gallus gallus ) are found in Madagascar, but it is unclear how they arrived there. Did they accompany the initial Austronesian-speaking populations that reached Madagascar via the Indian Ocean or were they late arrivals with Arabian and African sea-farers? To address this question, we investigated the mitochondrial DNA control region diversity of modern chickens sampled from around the Indian Ocean rim (Southeast Asia, South Asia, the Arabian Peninsula, East Africa and Madagascar). In contrast to the linguistic and human genetic evidence indicating dual African and Southeast Asian ancestry of the Malagasy people, we find that chickens in Madagascar only share a common ancestor with East Africa, which together are genetically closer to South Asian chickens than to those in Southeast Asia. This suggests that the earliest expansion of Austronesian-speaking people across the Indian Ocean did not successfully introduce chickens to Madagascar. Our results further demonstrate the complexity of the translocation history of introduced domesticates in Madagascar.

Dharmayanthi AB, Subagyo VNO, Nugraha RTP, Rahmini, Rahmadi C, Darmawan, Sutrisno H. 2022. Genetic characteristics and strain types of the invasive fall armyworm Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) in Indonesia. Biodiversitas 23: 3928-3935. The fall armyworm, Spodoptera frugiperda is an invasive pest in the tropical region of the western hemisphere, which is globally distributed, including in Indonesia. Therefore, this study aims to elucidate the genetic characteristics and strain types of the Indonesian population, based on mitochondrial and nuclear gene sequences. The haplotype diversity and phylogenetic trees were assessed according to the COI and COII gene sequences, where 381 bp of Tpi nuclear gene sequences were evaluated to define the strain types. The two haplotypes detected were within COI and COII, while the maximum likelihood tree based on COI gene sequences shows two clades related to rice and corn strain. Tpi gene sequences indicated that the populations belong to the corn strain, which suggested COI as a promising marker when complex inter-strain hybridization has not occurred. It was also discovered that mitochondrial and nuclear markers are inconsistent to define the strains.

Barbodes klapanunggalensissp. nov. is described on the basis of two specimens collected from the subterranean cave system of Klapanunggal karst area, Bogor Regency, West Java Province, Java Island, Indonesia. The new species is unique among its congeners in completely lacking eyes, its ocular vestige being marked by an orbital concavity fully covered with skin, and with no orbital rim. It also differs distinctly from most species of Barbodes by having relatively long paired fins (pectoral fin 26.0–31.4% SL; pelvic fin 21.5–24.4% SL), the adpressed tips of each overlapping the basal area of the adjacent posterior (pelvic and anal, respectively) fins; and the presence of a short pelvic axillary scale with a rounded posterior margin. Barbodes klapanunggalensissp. nov. is further distinguished from all congeners by the following combination of characters: head length 32.9–35.3% SL; pre-pectoral fin length 32.6–33.6% SL; pre-pelvic fin length 54.0–59.6% SL; anal-fin base length 9.7–11.8% SL; caudal peduncle depth 13.2–18.2% SL; completely nonpigmented body; and all fins with translucent interradial membranes and light cream to brownish rays. As reflected by its highly troglomorphic features, the new species is strictly adapted to cave habitats. Its small population size, coupled with a high level of potential threats to its known habitat, suggest that future conservation efforts will become necessary.

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is a major threat to amphibians, yet there are no reports of major disease impacts in East Asian frogs. Genetic variation of the major histocompatibility complex (MHC) has been associated with resistance to Bd in frogs from East Asia and worldwide. Using transcriptomic data collated from 11 Japanese frog species (one individual per species), we isolated MHC class I and IIb sequences and validated using molecular cloning. We then compared MHC from Japanese frogs and other species worldwide, with varying Bd susceptibility. Supertyping analysis, which groups MHC alleles based on physicochemical properties of peptide binding sites, identified that all examined East Asian frogs contained at least one MHC-IIb allele belonging to supertype ST-1. This indicates that, despite the large divergence times between some Japanese frogs (up to 145 million years), particular functional properties in the peptide binding sites of MHC-II are conserved among East Asian frogs. Furthermore, preliminary analysis using NetMHCIIpan-4.0, which predicts potential Bd-peptide binding ability, suggests that MHC-IIb ST-1 and ST-2 have higher overall peptide binding ability than other supertypes, irrespective of whether the peptides are derived from Bd, other fungi, or bacteria. Our findings suggest that MHC-IIb among East Asian frogs may have co-evolved under the same selective pressure. Given that Bd originated in this region, it may be a major driver of MHC evolution in East Asian frogs.

Ayam Cemani is a local Indonesian chicken with heavy pigmentation in plumage colour, skin, eyes, and inner body organs. This trait with dermal hyperpigmentation is identical to Fibromelanosis ( Fm ) mutation in a Silkie chicken. The causal mutation of the Fm trait is due to an inverted duplication and junction of two genomic regions involving the Endothelin3 ( EDN3 ) gene on chromosome 20. There are two duplication boundaries; one is specific to the Fm allele, the other is common for both Fm and fm ⁺ allele. Determining birds that are homozygous or heterozygous at this locus is useful for unifying the Fm trait of Cemani populations. This study develops a method for determining the presence or absence of Fm mutation by PCR amplification using the inverted sequences specific to the Fm allele. Further, it develops the restriction fragment length polymorphism (RFLP) method in regions common to the Fm and wild-type fm ⁺ allele. We aim to establish a simple method for detecting homozygous ( Fm / Fm ) and heterozygous ( Fm / fm ⁺ ) individuals with Fm mutation and to clarify the degree of fixation of the Fm trait in the Ayam Cemani populations and the association between the phenotype and genotype. The result showed that mostly, the phenotype for Cemani with Fm / fm ⁺ genotype is reddish black in their comb; meanwhile, the Cemani with ( Fm / Fm ) genotype showed heavy black pigmentation. Our study concluded that using the PCR-RFLP method. We can discriminate between Fm homozygous and heterozygous birds in the Cemani population. Thus, this briefly genotyping method effectively maintains and protects the pure line of Cemani chicken.