Biology subjects

Nishiumi, I.

Publications and source records attributed to Nishiumi, I..

4 recordsLinked to original sources

bioRxiv2026

The not-so-great speciator: Systematics and species limits in a rapid radiation, the Asiatic white-eye complex (Zosterops spp.)

Abstract/SummaryHere we untangle the systematics of the Asiatic white-eye complex (Zosterops spp.) to better understand the early stages of a recent island radiation. We adopt an integrative approach involving allelic data, genome-scale single nucleotide polymorphisms (SNPs), and museum-based morphometrics coupled with a comprehensive sampling to provide the most holistic understanding of the group to date. The island lineages of Asiatic white-eyes across Indonesia, the Philippines, East Asia, the adjacent oceanic islands of the Western Pacific underwent a deep split separating Zosterops everetti and Z. nigrorum in the Phillippines from a very rapid radiation including Z. japonicus, Z. meyeni, and Z. montanus in the Philippines, Japan, and Indonesia. Z. nigrorum catarmanensis on Camiguin South in the Philippines was found to be nested within Z. montanus and a species limit between Z. nigrorum populations on Panay and Luzon was strongly supported. Phylogenetic splits and population structure were detected within the clade containing Z. japonicus, Z. meyeni, and Z. montanus. A well-supported split separates a northern group including Northern Philippines Z. montanus subspecies, Z. meyeni, and Z. japonicus from the southerly Z. montanus taxa. This creates a paraphyletic Z. montanus. However, based on speciation rates within the broader Asiatic white-eye clade this break likely does not yet represent evolutionarily independent species lineages. Morphological evolution is taking place within the Asiatic white-eyes especially within the robust, large-billed subspecies of Z. japonicus on the oceanic islands of Japan and in the newly identified yellow-morph of Z. montanus on Camiguin South.

evolutionary biology↗

bioRxiv2025

DNA Specimen Preservation using DESS and DNA Extraction in Museum Collections: A Case Study Report

Recent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. DNA analysis has become an essential tool for taxonomic research and biodiversity assessment; however, freezer storage for all samples is impractical due to space limitations and operational costs. This creates a pressing need to develop more widely applicable DNA preservation methods. We investigated the comparative effects of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation on both morphology and DNA integrity using museum specimens from various taxonomic groups. Our results demonstrated that DESS preservation maintained high-quality DNA fragments exceeding >15 kb at room temperature across all examined species, with nematode samples maintaining DNA integrity even after 10 years of storage. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing. Simple SummaryRecent advances in DNA research have increased the necessity for museums to preserve not only morphological specimens but also their DNA, leading us to maintain tissue samples linked to specimens at -80{degrees}C. However, as freezer storage for all samples is impractical, there is a pressing need to develop more widely applicable DNA preservation methods. In this study, we investigated the effectiveness of traditional preservation methods versus DESS (DMSO/EDTA/saturated NaCl solution) preservation with regards to both morphology and DNA integrity using our museum specimens. Our results demonstrated that DESS preservation maintained high molecular weight DNA at room temperature across all examined species. When preserving whole organisms, the optimal preservation solution conditions for maintaining both morphological features and DNA integrity varied among species. Notably, DNA integrity was maintained even after complete evaporation of the DESS solution. These findings suggest that DESS utilization for specimen DNA preservation is effective across many species, not only for long-term storage in environments without freezer facilities but also for temporary preservation until freezing is possible.

zoology↗

bioRxiv2020

Examining the genetic influences of migratory status on island colonisation by naturally and recently established populations of a bird species

AimFounder effects and recurrent immigration are two major factors that potentially contribute to genetic differentiation and population persistence in the early-stage of remote island colonization. However, their relative importance remains controversial. By conducting population genetics analyses of multiple remote island populations of the bull-headed shrike established naturally within several decades, we examined the relative contributions of founder effects and recurrent immigration on these island populations. LocationJapan TaxonLanius bucephalus MethodsWe used 15 microsatellite loci to analyze the population genetics of four newly established island populations and five Japanese mainland populations. Allelic richness, heterozygosity, genetic differentiation, and the strength of the genetic bottleneck were compared among the islands. Two analyses, STRUCTURE and the DAPC, were conducted to assess the relative influence of founder effects and recurrent immigration on genetic differentiation. Temporal samples collected over eight years on Minami-Daito Island were used to detect any change in genetic structure due to recurrent immigration. ResultsThe founder effect strongly influenced genetic differentiation on the most remote oceanic island, Chichi-jima Island. However, this population became extinct 20 years after colonization, possibly owing to a lack of recurrent immigration. The founder effect moderately influenced a land-bridge island, Kikai-jima Island, indicating the presence of a relatively large founder population without recurrent immigration. Surprisingly, another distant oceanic island, Minami-Daito Island, was likely subject to multiple recurrent immigration events from the mainland, which obscured any genetic differentiation previously established by the founder effect. Main conclusionUnderlying the island-specific population dynamics of colonization, founder effects contributed to the genetic differentiation among the three studied island populations. Importantly, however, recurrent immigration strongly affected the population persistence and subsequent evolutionary processes of remote island populations, potentially overwhelming the founder effect. We argue the importance of recurrent immigration in highly remote island colonization, which has been previously overlooked.

ecology↗

bioRxiv2017

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Birds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Il-lumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.

ecology↗