Ibnu Maryanto

Multiple geographic origins of commensalism and complex dispersal history of black rats

The Black Rat (Rattus rattus) spread out of Asia to become one of the worlds worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA.

We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37–0.47 and 0.14–0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.

Phylogeny, diversity, and biogeography of Southeast Asian spiny rats (Maxomys).

Abstract Knowledge of the diversity and relationships of species in many groups of plants and animals in Southeast Asia is severely limited, preventing an integrative understanding of evolutionary and ecological processes in island archipelagos. We generated a 3-locus DNA sequence data set to estimate phylogenetic relationships among species and populations of Maxomys, a genus of rodents endemic to Southeast Asia. Our inclusion of Crunomys as a potential outgroup supported the monophyly of Crunomys, but the genus was deeply nested within Maxomys. Because of the relatively ancient divergences (mean uncorrected p-distances up to 0.15 in cytochrome-b sequences) among species of Maxomys and short branch lengths among basal lineages of the phylogeny, we obtained little support for the oldest relationships in Maxomys + Crunomys. However, our analyses revealed unrecognized diversity in the form of divergent populations both between and within islands and the presence of 2 potentially undescribed species from Sulawesi. The Maxomys and Crunomys of Sulawesi belonged to 4 clades sister to extralimital species, suggesting that repeated overwater dispersal between Sundaland–Philippines and Sulawesi was an important isolating mechanism in the history of this group.

Plant functional types and traits as biodiversity indicators for tropical forests: two biogeographically separated case studies including birds, mammals and termites

Multi-taxon surveys were conducted in species-rich, lowland palaeotropical and neotropical forested landscapes in Sumatra, Indonesia and Mato Grosso, Brazil. Gradient-directed transects (gradsects) were sampled across a range of forested land use mosaics, using a uniform protocol to simultaneously record vegetation (vascular plant species, plant functional types (PFTs) and vegetation structure), vertebrates (birds, mammals) and invertebrates (termites), in addition to measuring site and soil properties, including carbon stocks. At both sites similar correlations were detected between major components of structure (mean canopy height, woody basal area and litter depth) and the diversities of plant species and PFTs. A plant species to PFT ratio [spp.:PFTs] was the best overall predictor of animal diversity, especially termite species richness in Sumatra. To a notable extent vegetation structure also correlated with animal diversity. These surrogates demonstrate generic links between habitat structural elements, carbon stocks and biodiversity. They may also offer practical low-cost indicators for rapid assessment in tropical forest landscapes.

The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation.

The vestibular system maintains the body’s sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of echolocation.

Molecular Genetic Evidence for the Place of Origin of the Pacific Rat, Rattus exulans

Commensal plants and animals have long been used to track human migrations, with Rattus exulans (the Pacific rat) a common organism for reconstructing Polynesian dispersal in the Pacific. However, with no knowledge of the homeland of R. exulans, the place of origin of this human-commensal relationship is unknown. We conducted a mitochondrial DNA phylogeographic survey of R. exulans diversity across the potential natural range in mainland and Island Southeast Asia in order to establish the origin of this human-commensal dyad. We also conducted allozyme electrophoresis on samples from ISEA to obtain a perspective on patterns of genetic diversity in this critical region. Finally, we compared molecular genetic evidence with knowledge of prehistoric rodent faunas in mainland and ISEA. We find that ISEA populations of R. exulans contain the highest mtDNA lineage diversity including significant haplotype diversity not represented elsewhere in the species range. Within ISEA, the island of Flores in the Lesser Sunda group contains the highest diversity in ISEA (across all loci) and also has a deep fossil record of small mammals that appears to include R. exulans. Therefore, in addition to Flores harboring unusual diversity in the form of Homo floresiensis, dwarfed stegodons and giant rats, this island appears to be the homeland of R. exulans.

A review of the Murina cyclotis complex (Chiroptera: Vespertilionidae) with descriptions of a new species and subspecies

Until recently, the taxon Murina cyclotis was considered to be a widespread species, albeit one that exhibited considerable individual, sexual and geographical variation. Subsequently however, it was recognised that this taxon was in fact a complex of species. As such, in 2012, two larger forms were recognised as separate and distinct species, namely: M. peninsularis in the Sunda region and M. fionae in Laos and Vietnam. In the current paper, a new cryptic species of the cyclotis-complex is described from peninsular Thailand based on a combination of external, craniodental and genetic differences. In addition, the population previously referred to M. cyclotis from the Nicobar Islands is described as a new subspecies of this new species. Despite this work and the research of others, the taxonomy of M. cyclotis still requires further study. The description of M. peninsularis is emended and the extensive variation in its morphological characters is addressed. The diagnostic characters of each taxon, as well as the additional data on ecology, zoogeography, distribution, echolocation and genetics, where available, are summarised and discussed.

Description of a New Species of theRhinolophus trifoliatus-Group (Chiroptera: Rhinolophidae) from Southeast Asia

A new species of woolly horseshoe bat in the Rhinolophus trifoliatus species group is described from Sabah in Malaysian Borneo. Two specimens from Central and West Kalimantan, Indonesia are referred to this species. A fourth specimen from western Thailand is referable to this species but on the basis of ~10% genetic divergence at the cytochrome oxidase-I gene is described as a separate subspecies. Morphologically and acoustically the two subspecies are similar. With a forearm length of 52.90–54.70 mm, a skull length of 24.27–26.57 mm and a call frequency of 49.2–50.0 kHz, the new species overlaps in size and call frequency with the sympatric R. trifoliatus. However, it differs significantly in having a dark noseleaf and a uniformly dark brown pelage, resembling, but being intermediate in size between R. sedulus and R. luctus, which have a skull length of 18.99–20.17 and 26.35–32.07 mm, respectively. It also differs from R. trifoliatus in the shape and size of the rostral inflation. It can be distinguished from R. beddomei (forearm length 55.00–63.44 mm) and R. formosae (forearm length 53.85–62.40 mm), which are endemic to the Indian Subcontinent and Taiwan, respectively, by its relatively smaller body size. Acoustic and genetic data are included in the comparison between the species. Both character states support the conclusions based on morphology. Further surveys in intact evergreen forest together with a re-examination of museum specimens may reveal that this species is widespread in Southeast Asia.

A Recent Bat Survey Reveals Bukit Barisan Selatan Landscape as a Chiropteran Diversity Hotspot in Sumatra

Bukit Barisan Selatan National Park is one of the last refuges protecting intact forest and a representative mammalian fauna in Sumatra. However, knowledge of bat diversity in the area is limited. From 2010 to 2012, 47 bat species were recorded through a series of surveys in 12 localities within and around the national park. An additional six species from the area were identified from the mammal collection of the Museum Zoologicum Bogoriense, Indonesia. At least seven of the species reported in this study are new records for Sumatra, including Kerivoula krauensis, K. lenis, K. minuta, Murina rozendaali, Myotis horsfieldii, Myotis cf. borneoensis, and Rhinolophus borneensis/celebensis. Moreover, a finding of two distinct morphs of Chironax melanocephalus coexisting in the study area indicates another possible undescribed species. With 60 species, we consider Bukit Barisan Selatan Landscape to be a Southeast Asian bat diversity hotspot and of critical importance in maintaining bat diversity in Sumatra.

Morphological analysis of house mice, Mus musculus (Rodentia, Muridae) in Southern and Eastern Indonesia and Western Australia

ABSTRACT Univariate and multivariate statistical analysis of 14 skull, dentary and dental characters and five external characters recorded from 78 specimens of Mus musculus indicated the occurrence of two distinct forms in southern and eastern Indonesia. The two forms were distinct from Mus musculus domesticus in Western Australia. The more widespread form was attributed to M. m. castaneus which occurred on Bali, Lombok, Flores, Lembata, Alor, Kai, Banda, Neira, Timor and Roti islands. The other form all of which are new record for the reason from Kisar and Tanimbar Islands (which represent new distributional records for Mus musculus), differed consistently from M. m. castaneus. Descriminant Function Analysis (DFA) using a reduced set of five skull, dental and external characters correctly allocated 98% of individuals to their appropriate form; bulla length, C1M3 length and M1 length were important discriminants between the two forms. Unlike local populations of Western Australian M. m. domesticus, which morphologically differed significantly, the island populations of the widespread M. m., castaneus did not appear to differ significantly.