Local endemism and within‐island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (i) little differentiation of terrestrial organisms among continental shelf islands and (ii) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected to well‐sampled phylogeographic studies, leaving these biogeographic assumptions of connectivity largely untested. We analysed nine unlinked loci from shrews of the genus Crocidura from seven mountains and two lowland localities on the Sundaic continental shelf islands of Sumatra and Java. Coalescent species delimitation strongly supported all currently recognized Crocidura species from Sumatra (six species) and Java (five species), as well as one undescribed species endemic to each island. We find that nearly all species of Crocidura in the region are endemic to a single island and several of these have their closest relative(s) on the same island. Intra‐island genetic divergence among allopatric, conspecific populations is often substantial, perhaps indicating species‐level diversity remains underestimated. One recent (Pleistocene) speciation event generated two morphologically distinct, syntopic species on Java, further highlighting the prevalence of within‐island diversification. Our results suggest that both between‐ and within‐island speciation processes generated local endemism in Sundaland, supplementing the traditional view that the region's fauna is relictual and primarily governed by extinction.     

Characterization and Identification of Asexual Strains of Pythium Associated with Root Rot of Rose in Japan

This study was conducted to survey the distribution of asexual isolates of Pythium in rose production and to characterize and identify them. Asexual isolates with proliferating globose sporangia belong to group P according to the key of van der Plaats‐Niterink (1981; Monograph of the genus Pythium. Studies in Mycology, Vol. 21, Centraalbueau Voor Schimmelcultures, Baarn, The Netherlands). Group P isolates were recovered from rotted roots of both cutting and miniature roses cultured in rock wool and ebb‐and‐flow culture systems, respectively, throughout the main rose production area of Japan. The typical feature of the P group isolates was that they could grow fast at high temperature, at least 30 mm per 24 h at 35°C. There was no difference between the P group isolates and P. helicoides in morphology and size of sporangia and sporangial germination mode. The symptoms caused by the group P isolates were root rot, followed by leaf blight and plant death in severe cases. In restriction fragment length polymorphism analysis of the rDNA‐ITS region, the banding patterns with five of six enzymes were identical between group P and P. helicoides, the only difference being seen with HhaI. In direct amplification analysis of minisatellite‐region DNA with M13 primer, group P and P. helicoides shared three of five distinct bands. In contrast, P. oedochilum and P. ostracodes showed different banding patterns except for each one band. The results suggest that the group P isolates obtained from rose root rot may be asexual strains of P. helicoides.     

Activities of plant cell wall-degrading enzymes by bacterial soft rot of orchid

Soft rot by bacterial pathogens is one of the most widespread and destructive diseases on various plants including orchids throughout the world. The pathogenicity of the pathogens is reported to be mainly determined by massive production of plant cell wall-degrading enzymes (PCDE). In the previous work, we have isolated 20 isolates of bacterial soft rot from orchids collected in Yogyakarta Special Region and West Java province, Indonesia. In this study, we further confirmed them as pathogens by hypersensitive reaction assay on tobacco leaves followed by pathogenicity test on Phalaenopsis sp. The production of four major PCDE by qualitative plate assays including pectate lyase, polygalacturonase, cellulase and protease was also evaluated. Even though all the isolates were able to initiate soft rot symptom, our results showed two distinct groups which clustered as producing and non-producing PCDE. The 16S rDNA analysis revealed that the isolates belonged to the genera Pectobacterium, Klebsiella, Serratia, Enterobacter, Citrobacter, Providencia and Pseudomonas.     

Evolutionary novelty in a rat with no molars

Rodents are important ecological components of virtually every terrestrial ecosystem. Their success is a result of their gnawing incisors, battery of grinding molars and diastema that spatially and functionally separates the incisors from the molars. Until now these traits defined all rodents. Here, we describe a new species and genus of shrew-rat from Sulawesi Island, Indonesia that is distinguished from all other rodents by the absence of cheek teeth. Moreover, rather than gnawing incisors, this animal has bicuspid upper incisors, also unique among the more than 2200 species of rodents. Stomach contents from a single specimen suggest that the species consumes only earthworms. We posit that by specializing on soft-bodied prey, this species has had no need to process food by chewing, allowing its dentition to evolve for the sole purpose of procuring food. Thus, the removal of functional constraints, often considered a source of evolutionary innovations, may also lead to the loss of the very same traits that fuelled evolutionary diversification in the past.     

Carving out turf in a biodiversity hotspot: multiple,previously unrecognized shrew species co‐occur on Java Island,Indonesia

In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co‐occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100–117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South‐East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co‐occurring on one mountain. Differences in species' body size, use of above ground‐level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence.     

Repeated evolution of carnivory among Indo‐Australian rodents

Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo‐Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.