Specimen collection is essential for modern science

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

BACKGROUND

Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.

RESULTS

The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae.

CONCLUSIONS

While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

Another New Bent-toed Gecko, genus Cyrtodactylus Gray 1837 (Squamata: Gekkonidae), from Borneo

To reveal the diversity of Indonesian bent-toed geckos, we pay attention to Kalimantan (Borneo)an island which has received less attention than other Indonesian islands such as Sumatra, Java, Sulawesi, the Moluccas, and the Lesser Sunda archipelagos. About 30 years after Hikida (1990) described three new Cyrtodactylus from Borneo, four more species were described, namely C. limajalur and C. muluensis in 2019, and C. hantu and C. miriensis in 2021, all by Davis et al. Through examination of the collection at MZB and three addition specimens collected from Tawau, we found several undescribed species, one of which we describe here. This new species is easily differentiated from all other congeners by the combination of the following characters: maximum SVL of at least 65.8 mm; no tubercles on dorsal surface of upper arm; tubercles present in the ventrolateral body folds; 2830 paravertebral tubercles; 1720 longitudinal dorsal tubercle rows; 3946 ventral scale rows at midbody; 1719 subdigital lamellae on fourth toe; precloacal pit with 57 pores in males arranged in a wide -shape but absent in females; no enlarged transverse median subcaudals; paired dark brown semilunar-shaped markings on the upper nape. Further study is needed to reveal its molecular phylogenetic position and biogeographical history.

Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using F_ST and d_xy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high F_ST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

Investigation of heavy metals on water quality and sediment: A case study Bireuen, Aceh Utara and Lhokseumawe City

Environmental pollution around the world in the last 10 years has continued to increase with increasing industrial growth. Environmental pollution has reduced the availability of clean water. Clean water is the main thing for all living things on this earth. Therefore, environmental pollution that occurs in the clean water crisis must be handled as soon as possible and reduced by various effective policies. The main focus of this research is to analyze heavy metal pollution on the surface of the water, clean water, and sediments caused by industrial activities. This research is a field study by taking samples directly at the location and then analyzing them in the laboratory. The results of the analysis showed that the highest heavy metal Fe on the water surface was found in Bireuen Regency by 0.28% compared to Lhokseumawe City with 0.0029% and Aceh Utara 0.0029%. Meanwhile, the highest heavy metals contained in clean water were recorded in Bireuen and Lhokseumawe City at 0.007% and 0.0064%, respectively. The results of the heavy metal analysis in the highest sediment were found in North Aceh at 42.93% compared to 8.02% and 18.12% for Bireuen and Lhokseumawe. Overall, the analysis carried out in this study shows that the surface water, clean water, and sediments have been contaminated by heavy metals. Meanwhile, the quality standard for surface water is 0.3 mg/l, net ai is 1.0 mg/l, and sediment is 20bj.

Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity

Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

A molecular genetic approach for sex determination on helmeted hornbill (Rhinoplax vigil) casque: a forensic casework

Helmeted Hornbill(Rhinolax vigil)is the only hornbill that equipped with solid casque made from keratin for both males and females. The demand for casque in the black market was huge and resulted in IUCN status leaped up from vulnerable to critically endangered. We received a total of 68 confiscated helmeted hornbill casques. As part of the casework and the objectives of the study, we determined to reveal the sex status of those casques and the best methods to work with keratinous material. Molecular methods to determining sex in birds rely on the CHD gene located on male and female chromosomes ZZ and ZW, respectively. We optimized laboratory protocols for genetic sexing using three independent sets of primers P2/P8, 2550F/2718R, and CHD1F/CHD1R to amplify regions of the sexlinked CHD-Z and CHD-W genes. The CHD1F/CHD1R determined sex 80.88% of samples. The 2550F/2718R were quite successful, sexing 51.47% of samples. In contrast, the P2/P8 only identified the sex around 20.58% of samples. These results showed that CHD1F/CHD1R works the most effective for sexing the casques with 52.9% females, 27.9% males, and 19.1% unidentified. Therefore, the most accurate and suitable primers are CHD1F/CHD1R, 2550F/2718R, and P2/P8, respectively for keratinous samples.