Search

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. [ABSTRACT FROM AUTHOR]

After nearly a decade of field inventories in which we preserved voucher specimens of the small terrestrial mammals of Sulawesi, we combined qualitative and quantitative analyses of morphological traits with molecular phylogenetics to better understand the diversity of shrews (Soricidae: Crocidura) on the island. We examined the morphology of 1368 specimens and obtained extensive molecular data from many of them, including mitochondrial DNA sequences from 851 specimens, up to five nuclear exons from 657 specimens, and thousands of ultraconserved elements from 90 specimens. By iteratively testing species limits using distinct character datasets and appropriate taxon sampling, we found clear, mostly consistent evidence for the existence of 21 species of shrews on Sulawesi, only seven of which were previously recognized. We divide these 21 species into five morphogroups, provide emended diagnoses of the seven previously named species, and describe 14 new species. The Long-Tailed Group contains Crocidura caudipilosa, C. elongata, C. microelongata, new species, and C. quasielongata, new species; the Rhoditis Group contains C. rhoditis, C. pseudorhoditis, new species, C. australis, new species, and C. pallida, new species; the Small-Bodied Group contains C. lea, C. levicula, C. baletei, new species, C. mediocris, new species, C. parva, new species, and C. tenebrosa, new species; the Thick-Tailed Group contains C. brevicauda, new species and C. caudicrassa, new species; and the Ordinary Group contains C. musseri, C. nigripes, C. normalis, new species, C. ordinaria, new species, and C. solita, new species. Documenting these endemic species reveals a local radiation (20 of the 21 species are members of an endemic clade) in which elevational gradients played a prominent role in either promoting speciation, or at a minimum, fostering the cooccurrence of phenotypically similar species. As now understood, the species-level diversity of Crocidura on Sulawesi is nearly three times the known diversity of any other insular shrew fauna. This study highlights the fact that if we wish to understand the true extent of biodiversity on Earth, large-scale, vouchered organismal inventories followed up with thorough examinations of genetic, morphological, and geographic traits are sorely needed in montane tropical regions, even for purportedly well-studied groups such as mammals. [ABSTRACT FROM AUTHOR]

Sulawesi is the largest, most topographically complex island in the Wallacean biogeographic zone, and it has a rich fauna of endemic small mammals, dominated by rodents of the family Muridae. Among murids, the Bunomys division is the most species‐rich radiation on Sulawesi. In total, the division contains 11 genera and 32 species, five and 20 of which are endemic to Sulawesi. We combined a five‐locus phylogeny and linear cranial morphology to better understand the taxonomy and local scales of endemism within the Bunomys division on Sulawesi. Phylogenetic analyses of mitochondrial and nuclear DNA placed B. fratrorum among other genera and inferred Paruromys as sister to the type species of Taeromys (T. celebensis). We resolve these issues by resurrecting Frateromys, a genus under which B. fratrorum was once placed, and returning Paruromys dominator to Taeromys. Within three species, F. fratrorum, T. callitrichus, and T. taerae, we recovered Pleistocene age divergences between populations sampled across the northern peninsula of Sulawesi; divergence between western and eastern populations of F. fratrorum may reflect the existence of two species. [ABSTRACT FROM AUTHOR]

The Indonesian island of Sulawesi is home to a diverse range of small mammal species, with 73 of them found nowhere else in the world. However, many of these species are threatened or poorly studied. To address this, the IUCN Species Survival Commission (SSC) Small Mammal Specialist Group organized a workshop to update the Red List assessments for these species and identify conservation and research needs. The workshop highlighted the need for improved knowledge of distribution, ecology, and threats to these species, as well as increased area protection and community involvement in conservation efforts. Overall, there is still much work to be done to understand and protect Sulawesi's unique small mammal fauna. [Extracted from the article]

The Indonesian island of Sulawesi is a globally significant biodiversity hotspot with substantial undescribed biota, particularly blood-borne parasites of endemic wildlife. Documenting the blood parasites of Sulawesi's murine rodents is the first fundamental step towards the discovery of pathogens likely to be of concern for the health and conservation of Sulawesi's endemic murines. We screened liver samples from 441 specimens belonging to 20 different species of murine rodents from 2 mountain ranges on Sulawesi, using polymerase chin reaction (PCR) primers targeting the conserved 18S rDNA region across the protozoan class Kinetoplastea. We detected infections in 156 specimens (10 host species) with a mean prevalence of 35.4% (95% confidence interval [CI] = 30.9–39.8%). Sequences from these samples identified 4 infections to the genus Parabodo, 1 to Blechomonas, and the remaining 151 to the genus Trypanosoma. Within Trypanosoma, we recovered 17 haplotypes nested within the Trypanosoma theileri clade infecting 117 specimens (8 host species) and 4 haplotypes nested within the Trypanosoma lewisi clade infecting 34 specimens (6 host species). Haplotypes within the T. theileri clade were related to regional Indo-Australian endemic trypanosomes, displayed geographic structuring but with evidence of long-term connectivity between mountains, and had substantial phylogenetic diversity. These results suggest T. theileri clade parasites are native to Sulawesi. Conversely, T. lewisi clade haplotypes were recovered from both endemic and introduced rodents, demonstrated complete geographic separation between clades, and had low genetic diversity. These results suggest that the T. lewisi clade parasites invaded Sulawesi recently and likely in 2 separate invasion events. Our results provide the first records of metakinetoplastids in Sulawesi's rodents and highlight the need for more extensive sampling for pathogens in this biodiversity hotspot. [ABSTRACT FROM AUTHOR]

We describe a new species of Crocidura (Soricidae) from Sulawesi Island, Indonesia, documenting its novelty with both genetic and morphological characters. The new species is widespread on the island, with vouchered records from nine general localities distributed among five of the island's areas of endemism. Morphologically, the new species is readily distinguished from all other described Sulawesi Crocidura by its intermediate body size, gray pelage, and long, hairy tail. The new species was mainly captured in pitfalls placed in the ground, but we also obtained evidence that it readily climbs trees and may be scansorial in its locomotor habits. Populations of the new species sampled from across the island are closely related, separated by < 0.02 uncorrected mitochondrial p -distances. The new species is one member of an endemic radiation of shrews on Sulawesi now known to contain six valid species and several undescribed species, all within the genus Crocidura. Resolution of species limits and phylogenetic relationships in this radiation is hindered by habitat loss at type localities, historical designation of new species using very small sample sizes, and a lack of genetic data from type specimens. Kami mendeskripsikan spesies baru Crocidura (Soricidae) dari Pulau Sulawesi, Indonesia, sekaligus mendokumentasikan keunikan karakter secara genetik maupun morfologi dari spesies tersebut. Spesies baru ini tersebar luas di Pulau Sulawesi, diketahui berdasarkan spesimen yang berasal dari sembilan lokasi umum yang tersebar di lima kawasan endemik di pulau tersebut. Secara morfologi, spesies baru ini dapat dibedakan dari spesies Crocidura lainnya dari Sulawesi berdasarkan ukuran tubuh yang sedang, rambut tubuh berwarna abu-abu, dan ekor yang panjang dan berambut. Spesies baru ini sebagian besar diperoleh dari perangkap sumuran yang ditanam didalam tanah, selain itu kami juga mendapatkan bukti bahwa spesies ini mampu memanjat pohon dan kemungkinan memiliki perilaku sebagai pemanjat. Beberapa populasi spesies yang dikoleksi dari Sulawesi ini mempunyai kekerabatan yang dekat, hanya dipisahkan oleh jarak proporsi DNA mitokondria (tidak terkoreksi) sebesar < 0.02. Spesies baru ini merupakan salah satu anggota dari suatu kelompok radiasi endemik cecurut di Sulawesi yang sampai saat ini diketahui terdiri atas enam spesies yang valid, dan beberapa spesies yang belum dideskripsikan, semuanya termasuk didalam genus Crocidura. Kepastian dalam menetapkan batasan jarak antar spesies dan hubungan kekerabatan genetik dari radiasi kelompok cecurut di Sulawesi terkendala oleh kerusakan habitat pada lokasi spesimen tipe, sejarah penamaan spesies yang hanya berdasarkan sampel yang sedikit, dan keterbatasan data molekuler dari spesimen tipe. [ABSTRACT FROM AUTHOR]

Aim: To determine the historical dynamics of colonization and whether the relative timing of colonization predicts diversification rate in the species‐rich, murine rodent communities of Indo‐Australia. Location: Indo‐Australian Archipelago including the Sunda shelf of continental Asia, Sahul shelf of continental Australia, the Philippines and Wallacea of Indonesia. Taxon: Order Rodentia, Family Muridae. Methods: We used a fossil‐calibrated molecular phylogeny and Bayesian biogeographical modelling to infer the frequency and temporal sequence of biogeographical transitions among Sunda, Sahul, the Philippines and Wallacea. We estimated diversification rates for each colonizing lineage using a method‐of‐moments estimator of net diversification and Bayesian mixture model estimates of diversification rate shifts. Results: We identified 17 biogeographical transitions, including nine originating from Sunda, seven originating from Sulawesi and broader Wallacea and one originating from Sahul. Wallacea was colonized eight times, the Phillipines five times, Sunda twice and Sahul twice. Net diversification rates ranged from 0.2 to 2.12 species/lineage/My with higher rates in secondary and later colonizers than primary colonizers. The highest rates were in the genus Rattus and their closest relatives, irrespective of colonization history. Main Conclusions: Our inferences from murines demonstrate once again the substantial role of islands as sources of species diversity in terrestrial vertebrates of the IAA with most speciation events occurring on islands. Sulawesi and broader Wallacea have been a major source of colonists for both island and continental systems. Crossings of Wallace's Line were more common than subsequent transitions across Lydekker's Line to the east. While speciation following colonization of oceanic archipelagos and large islands is consistent with adaptive radiation theory and ideas regarding ecological opportunity, we did not observe a strong signal of incumbency effects. Rather, subsequent colonists of landmasses radiated unhindered by previous radiations. [ABSTRACT FROM AUTHOR]

Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew ( Crocidura elongata ) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C . elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata , like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs. [ABSTRACT FROM AUTHOR]

We document a new genus and species of rodent (Muridae) from the west-central region of Sulawesi Island, Indonesia. The new taxon is known only from the type locality at around 1,600 m elevation on Mt. Gandangdewata of the Quarles Range, in the district of Mamasa. With phylogenetic analyses of DNA sequences from 5 unlinked loci, we infer that the new taxon is sister to the Sulawesi water rat, Waiomys mamasae, and nested within a clade of rodents from Sulawesi that otherwise feed exclusively on invertebrates. The new species is distinguishable from other rodents of Sulawesi by the combination of its small, slender body; soft, gray-brown fur; small, rounded ears; long, sparsely haired tail; long, fine mystacial vibrissae; gracile cranium; short rostrum; pronounced lacrimal bone; prominent, sickle-shaped coronoid process; and pale orange enamel on labial surface of incisors. Unlike its closest relatives, the new species feeds on both plant and animal matter, and may represent a rare evolutionary reversal of traits associated with a carnivorous diet in murids. [ABSTRACT FROM AUTHOR]