Phylogenetic and genetic variation of common mudskippers (Periophthalmus kalolo Lesson, 1831) from the southern coast of Java, Indonesia inferred from the COI mitochondrial gene.

BACKGROUND: The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach). RESULTS: The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events. CONCLUSIONS: These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.

Phylogenetic and genetic variation analysis of lesser short-nosed fruit bat Cynopterus brachyotis (Müller 1838) on Java island, Indonesia, inferred from mitochondrial D-loop.

BACKGROUND: Cynopterus brachyotis (Müller 1838) is a generalist and widespread fruit bat species which inhabits different types of habitats in Southeast Asia. This species plays an essential role as a seed disperser and pollinator. Morphological study and phylogenetic analysis using mtDNA markers (cyt-b and D-loop) revealed that this species had two different forms in peninsular Malaysia and Borneo and six lineages in Southeast Asia that lead to new species formation. In addition, this species is also reported to have high genetic diversity in Malaysia and Thailand based on the D-loop sequence. However, a phylogenetic and genetic variation study of C. brachyotis in Indonesia has not been conducted yet. These two studies are important as additional information for taxonomic and population genetic studies of this species. Thus, we performed the phylogenetic and genetic diversity analysis of the C. brachyotis population collected from seven habitats on Java island, including open-fragmented habitats (urban, coffee and rubber plantations, pine forest, secondary forest, mangrove forest) and closed habitats (natural forest) using the mtDNA D-loop marker. RESULTS: The phylogenetic tree using the Bayesian inference (BI) and genetic distance using the Kimura-2 parameter (K-2P) demonstrated that 33 individuals of C. brachyotis from seven habitats on Java island overlapped between habitats and could not be distinguished according to their habitats and lineage. Intrapopulation and intraspecies analysis revealed high haplotype diversity of this species on Java island (Hd = 0.933-1.000). The haplotype network was split into two haplogroups, showing haplotype sharing between habitats. These phylogenetic and genetic variations analysis of C. brachyotis bats on Java island indicated that this species is widespread and adapt to different habitats. CONCLUSIONS: This study of C. brachyotis on Java island collected from seven different habitats has overlapped and genetically close and has high genetic variation. Our results provide the first reported study of C. brachyotis on Java island and provide data to understand the phylogenetic and genetic diversity of this species in Indonesia.

Health comparison between guinea pigs raised in uncontrolled and controlled environments.

Background and Aim: Guinea pigs (GPs) (Cavia porcellus) are not only kept as pets but also widely used in biological and biomedical research. At present, GPs are also used as a species for animal-assisted therapy (AAT). Consequently, assessing their health status is vital to determining their quality of life, usability for research, and prevention of spread of potential zoonotic diseases to patients using them for AAT. GPs are mainly sourced from animal markets supplied by traditional farms, where environmental factors and sanitation are not properly controlled. This study aimed to compare health status between GPs raised in uncontrolled (conventional farm) and controlled (animal facility) environments. Materials and Methods: Sample animals were obtained from a local animal market and transported to an animal facility. After 1 week of acclimatization, the health status of the animals, including general health condition, body weight, body temperature, complete blood count, liver function (alanine aminotransferase and bilirubin), renal function (blood urea nitrogen and creatinine), and presence of ectoparasites and endoparasites, was assessed. Then, the animals were maintained in the animal facility following the standard procedure for laboratory animals. After 2 months, the animals' health status was re-examined, assessing the same parameters. Results: Based on the evaluated parameters, GPs raised in an uncontrolled environment were found to have poorer health status than those raised in a controlled environment. There were significant differences in almost all parameters between GPs raised in controlled and uncontrolled environments. We found that the populations of two ectoparasites, Gyropus ovalis and Gliricola porcelli, and one endoparasite, Eimeria caviae, decreased significantly following the movement of the animals from an uncontrolled to a controlled environment. Conclusion: GPs raised in an uncontrolled environment have poor health status. However, a controlled environment with better care management can improve the health status of GPs.

Genetic Diversity of Amylomyces rouxii from Ragi tapai in Java Island Based on Ribosomal Regions ITS1/ITS2 and D1/D2.

Amylomyces rouxii is commonly found as amylolytic fungi in tapai fermentation. However, its diversity is rarely reported despite being often used for food production in Southeast Asia. This research aims to analyze the genetic diversity and the distribution pattern of A. rouxii from Ragi tapai in Java Island, Indonesia. We isolated the fungus from samples obtained from Ragi tapai producing centers in Bandung, Sumedang, Muntilan, Blora, Yogyakarta, and Bondowoso. The obtained isolates were molecularly identified based on the ribosomal regions ITS1/ITS2 and D1/D2, then analyzed for phylogenetic tree reconstruction, genetic distance, genetic variation, and haplotype networking. Six isolates showed specific morphological traits of A. rouxii. However, phylogenetic tree reconstruction on the ribosomal genes showed that the isolates were grouped into two different clades related to two species. Clade A included BDG, SMD, and MTL isolates related to A. rouxii, whereas clade B included YOG, BLR, and BDS isolates related to Mucor indicus. The genetic distances between clades for ITS1/ITS2 and D1/D2 were 0.6145 and 0.1556, respectively. In conclusion, we confirmed the genetic diversity of molds from Ragi tapai in Java Island and showed that the isolates are not only related to A. rouxii as reported before.

A tiny new species of Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from Belitung Island and Southeastern Sumatra, Indonesia.

A tiny new species of narrow-mouthed frog of the genus Microhyla is described from the island of Belitung and southeastern Sumatra, Indonesia. The most distinctive feature of the new frog is its diminutive adult size, snout-vent length ranging only from 12.3 to 15.8 mm in adult males. Phylogenetic analyses based a fragment of the mitochondrial 16S rRNA gene, along with detailed morphological and acoustic comparison differentiate the new taxon from all known congeners. The new species, formally described as Microhyla sriwijaya sp. nov., is a member of the M. achatina species group and the sister taxon to M. orientalis. It is diagnosable from other congeners by a combination of characters: (1) smaller male snout-vent size 16 mm; (2) snout obtusely rounded in dorsal view; (3) absence of mid-dorsal line and skin fold; (4) first finger reduced (finger I length less than half of finger II length); (5) dorsum with a prominent dark median mark extending posteriorly, narrow anteriorly near the level of the shoulder and expanding dorsolaterally up to the vent; margins of the dorsal marking concave with broad reddish-brown or orange colouration on either side; (6) foot webbing rudimentary, reaching just up to the first subarticular tubercle on all toes; (7) dorsal skin with prominent tubercles, especially in life; (8) tibiotarsal articulation of adpressed limb reaching beyond the snout tip; and (9) males produce a single type of call with pulsatile temporal structure, calls of relatively short duration ranging between 31.862.8 s, with two to three pulses delivered at a rate ranging between 32.236.0 pulses per second, and the mean overall dominant frequency of 4.3 kHz. The uncorrected pairwise genetic distances between Microhyla sriwijaya sp. nov. and all other known congeners are > 3.8% for the studied 16S gene fragment. The new species was discovered from wayside rural areas with oil palm plantations at four localities in the small island of Belitung (type locality), and from coffee plantation and secondary forest at Lampung in southeastern Sumatra. It is not known from any protected area and appears to be threatened due to tin mining activity, intensive logging, oil palm, and other commonly practiced agriculture activities.