48 Works

Data from: Heme pathway evolution in kinetoplastid protists

Ugo Pierre Cenci, Daniel Moog, Bruce A. Curtis, Goro Tanifuji, Laura Eme, Julius Lukeš & John M. Archibald
Background: Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetoplastids have emerged from free-living, non-pathogenic ancestors on multiple occasions during the evolutionary history of the group. Interestingly, in both parasitic and free-living kinetoplastids, the heme pathway—a core metabolic pathway in a wide range of organisms—is incomplete or entirely absent. Indeed, Kinetoplastea investigated thus far...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploid Arabidopsis kamchatica

Timothy Paape, Masaomi Hatakeyama, Rie Shimizu-Inatsugi, Teo Cereghetti, Onda Yoshihiko, Tanaka Kenta, Jun Sese & Kentaro K. Shimizu
Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator A. halleri and of the nonaccumulator A. lyrata. We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high...

Phage origin of mitochondrion-localized family A DNA polymerases in kinetoplastids and diplonemids

Yuji Inagaki & Ryo Harada
Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in...

SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq)

Mengying Cai
Our study is the first to explore the genetic composition of ancient Cryptomeria trees across distribution range in China. Background and Objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and...

Data from: Species asynchrony and response diversity determine multifunctional stability of natural grasslands

Takehiro Sasaki, Xiaoming Lu, Mitsuru Hirota & Yongfei Bai
1. A growing body of empirical evidence has suggested that biodiversity affects the simultaneous performance of multiple ecosystem functions (that is, ecosystem multifunctionality). Given increasing environmental variability and uncertainty under global change, an emerging question is how biodiversity influences the stability of multiple functions (that is, multifunctional stability). We currently know little, however, about the determinants and mechanisms of multifunctional stability, which is of practical importance for ensuring the sustainable provision of multiple functions. 2....

Datasets for phylogenetic analyses of Pavlomulina ranunculiformis

Ryoma Kamikawa, Masanobu Kawachi, Takuro Nakayama, Motoki Kayama, Mami Nomura, Hideaki Miyashita, Othman Bojo, Lesley Rhodes, Stuart Sym, Richard Pienaar, Ian Probert & Isao Inouye
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton, which is responsible for around 50% of global net primary production. However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads are a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences. The phenotypic identity of this group, which does not...

Data from: Regional difference in sex steroid action on formation of morphological sex differences in the anteroventral periventricular nucleus and principal nucleus of the bed nucleus of the stria terminalis

Moeko Kanaya, Mumeko C. Tsuda, Shoko Sagoshi, Kazuyo Nagata, Chihiro Morimoto, Chaw Kyi Tha Thu, Katsumi Toda, Shigeaki Kato, Sonoko Ogawa & Shinji Tsukahara
Sex steroid action is critical to form sexually dimorphic nuclei, although it is not fully understood. We previously reported that masculinization of the principal nucleus of the bed nucleus of the stria terminalis (BNSTp), which is larger and has more neurons in males than in females, involves aromatized testosterone that acts via estrogen receptor-α (ERα), but not estrogen receptor-β (ERβ). Here, we examined sex steroid action on the formation of the anteroventral periventricular nucleus (AVPV)...

Highly mobile seed predators contribute to interisland seed dispersal within an oceanic archipelago

Haruko Ando, Yuka Mori, Miho Nishihiro, Kanon Mizukoshi, Masaki Akaike, Wataru Kitamura & Nozomu J. Sato
Long-distance dispersal (LDD) is an essential event for species colonization and expansion in oceanic island ecosystems. Endozoochory by birds is an important factor promoting the LDD of plant seeds, but its contribution to interisland seed dispersal is still unclear. Here, we show possible seed dispersal by a seed predator pigeon, the Japanese wood pigeon Columba janthina, among oceanic islands in the Izu archipelago, Japan. Although some previous studies showed that most seeds swallowed by this...

Data from: Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

Yuji Inagaki, Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Tazuya Takahashi, Hideaki Miyashita, Ken-Ichiro Ishida, Mitsunori Iwataki, Euki Yazaki & Eriko Matsuo
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet...

Data from: The potential role of temperate Japanese regions as refugia for the coral Acropora hyacinthus in the face of climate change

Aki Nakabayashi, Takehisa Yamakita, Takashi Nakamura, Hiroaki Aizawa, Yuko F. Kitano, Akira Iguchi, Hiroya Yamano, Satoshi Nagai, Sylvain Agostini, Kosuke M. Tshima & Nina Yasuda
As corals in tropical regions are threatened by increasing water temperatures, poleward range expansion of reef-building corals has been observed, and temperate regions are expected to serve as refugia in the face of climate change. To elucidate the important indicators of the sustainability of coral populations, we examined the genetic diversity and connectivity of the common reef-building coral Acropora hyacinthus along the Kuroshio Current, including recently expanded (<50 years) populations. Among the three cryptic lineages...

Data from: Worldwide core collections of tea (Camellia sinensis) based on SSR markers

Fumiya Taniguchi, Keiko Kimura, Tetsuji Saba, Akiko Ogino, Satoshi Yamaguchi & Junichi Tanaka
Tea (Camellia sinensis (L.) O. Kuntze) is the world’s most popular beverage crop. However, to date, no core collection has been selected from worldwide germplasm resources on the basis of genotype data. In this study, we analyzed 788 tea germplasm accessions using 23 simple sequence repeat (SSR) markers. Our population structure analysis divided the germplasms into a Japanese group and an exotic group. The latter could be divided into var. sinensis and var. assamica. The...

Data from: The effect of sitagliptin on carotid artery atherosclerosis in Type 2 Diabetes: the PROLOGUE randomized controlled trial

Jun-Ichi Oyama, Koichi Node, Atsushi Tanaka, Toyoaki Murohara, Masafumi Kitakaze, Tomoko Ishizu, Yasunori Sato, Haruo Kamiya, Masaharu Ishihara, Koji Maemura, Hirofumi Tomiyama, Yukihito Higashi, Hirotsugu Yamada, Kentaro Yamashita, Yasuko K. Bando, Shinichiro Ueda & Teruo Inoue
Background: Experimental studies have suggested that dipeptidyl peptidase-4 (DPP-4) inhibitors provide cardiovascular protective effects. We performed a randomized study to evaluate the effects of sitagliptin added on to the conventional therapy compared with conventional therapy alone (diet, exercise, and/or drugs, except for incretin-related agents) on the intima-media thickness (IMT) of the carotid artery, a surrogate marker for the evaluation of atherosclerotic cardiovascular disease, in people with type 2 diabetes mellitus (T2DM). Methods and Findings: We...

Data from: Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Michelle M. Leger, Martin Kolisko, Ryoma Kamikawa, Courtney W. Stairs, Keitaro Kume, Ivan Čepička, Jeffrey D. Silberman, Jan O. Andersson, Feifei Xu, Akinori Yabuki, Laura Eme, Qianqian Zhang, Kiyotaka Takishita, Yuji Inagaki, Alastair G. B. Simpson, Tetsuo Hashimoto & Andrew J. Roger
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed....

Data from: Geographical variation in the heterogeneity of mutualistic networks

Shoko Sakai, Sören Metelmann, Yukihiko Toquenaga & Arndt Telshow
Plant–animal mutualistic networks are characterized by highly heterogeneous degree distributions. The majority of species interact with few partner species, while a small number are highly connected to form network hubs that are proposed to play an important role in community stability. It has not been investigated, however, if or how the degree distributions vary among types of mutualisms or communities, or between plants and animals in the same network. Here, we evaluate the degree distributions...

Data from: Mapping of genetic factors that elicit intermale aggressive behavior on mouse chromosome 15: intruder effects and the complex genetic basis

Aki Takahashi, Hiroki Sugimoto, Shogo Kato, Toshihiko Shiroishi & Tsuyoshi Koide
Despite high estimates of the heritability of aggressiveness, the genetic basis for individual differences in aggression remains unclear. Previously, we showed that the wild-derived mouse strain MSM/Ms (MSM) exhibits highly aggressive behaviors, and identified chromosome 15 (Chr 15) as the location of one of the genetic factors behind this escalated aggression by using a panel of consomic strains of MSM in a C57BL/6J (B6) background. To understand the genetic effect of Chr 15 derived from...

Changes in arthropod community but not plant quality benefit a specialist herbivore on plants under reduced water availability

Po-An Lin, Chia-Ming Liu, Jia-Ang Ou, Cheng-Han Sun, Wen-Po Chuang, Chuan-Kai Ho, Natsuko Kinoshita & Gary Felton
Plants growing under reduced water availability can affect insect herbivores differently, in some instances benefitting them. However, the forces mediating these positive impacts remain mostly unclear. To identify how water availability impacts plant quality and multitrophic interactions, we conducted manipulative field studies with two populations of the specialist herbivore Pieris rapae, and its host plant, Rorippa indica. We found that P. rapae larvae experienced higher survival on R. indica growing under low water availability compared...

Nature, agriculture and rural resilience: Interdependencies between natural protected areas and rural landscapes in Satoyama/Satoumi in Japan

Maya N. Ishizawa
The Capacity Building Workshops on Nature-Culture Linkages in Heritage Conservation (CBWNCL), held at the University of Tsukuba in Japan, gather Asia-Pacific heritage professionals with the aim of creating a platform of mutual-learning and exchange between the culture and nature sectors. In the first workshop on Agricultural Landscapes, from 14 case studies, 5 showed natural protected areas in tense relations with their rural landscape surroundings. However, these agricultural landscapes are essential for protecting natural values, as...

Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

Richard W. Hill, Eric J. Armstrong, Kazuo Inaba, Masaya Morita, Martin Tresguerres, Jonathon H. Stillman, Jinae N. Roa & Garfield T. Kwan
The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of...

Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

Kyoko Aoki, Ichiro Tamaki, Katsuhiro Nakao, Saneyoshi Ueno, Takashi Kamijo, Hiroaki Setoguchi, Noriaki Murakami, Makoto Kato & Yoshihiko Tsumura
Climatic changes have played major roles in plants’ evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants’ populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter...

Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female Drosophila melanogaster

Ryusuke Niwa, Yuto Yoshinari, Tomotsune Ameku, Shu Kondo, Hiromu Tanimoto, Takayuki Kuraishi & Yuko Shimada-Niwa
Stem cells fuel the development and maintenance of tissues. Many studies have addressed how local signals from neighboring niche cells regulate stem cell identity and their proliferative potential. However, the regulation of stem cells by tissue-extrinsic signals in response to environmental cues remains poorly understood. Here we report that efferent octopaminergic neurons projecting to the ovary are essential for germline stem cell (GSC) increase in response to mating in female Drosophila. The neuronal activity of...

Data from: Inbreeding tolerance as a pre-adapted trait for invasion success in the invasive ant Brachyponera chinensis

Pierre-André Eyer, Kenji Matsuura, Edward Vargo, Kazuya Kobayashi, Toshihisa Yashiro, Wataru Suehiro, Chihiro Himuro, Tomoyuki Yokoi, Benoit Guénard, Robert R. Dunn, Kazuki Tsuji, Pierre‐André Eyer & Edward L. Vargo
Identifying traits that facilitate species introductions and successful invasions of ecosystems represents a key issue in ecology. Following their establishment into new environments, many non-native species exhibit phenotypic plasticity with post-introduction changes in behavior, morphology or life history traits that allow them to overcome the presumed loss of genetic diversity resulting in inbreeding and reduced adaptive potential. Here we present a unique strategy in the invasive ant Brachyponera chinensis (Emery), in which inbreeding tolerance is...

Data from: A simple micropump based on a freeze-dried superabsorbent polymer for multiplex solution processing in disposable devices

Gokul Chandra Biswas, , Takekoshi Kazuhiro & Hiroaki Suzuki
We describe a simple micropump for disposable microfluidic devices. The pump is constructed using a freeze-dried disc of a superabsorbent polymer (SAP). The disc absorbs a solution in a flow channel and swells upward in a pumping chamber. Despite the simple structure of this device, the rate of absorption remains constant and can be adjusted by changing the composition of the SAP, its size, the dimensions of the flow channel, and the medium to be...

Data from: Digging out intersexual and meteorological effects on cicada emergence using 10-year citizen monitoring

Wataru Mukaimine, Kazutaka Kawatsu & Yukihiko Toquenaga
Understanding the mechanisms behind the seasonal emergences of herbivorous insects is ecologically important. However, little is known about the effect of meteorological factors and the other individuals in cicada emergence timing in fluctuating environments. Particularly, due to the long lifecycle and subterranean larval stages of cicada species, investigating their seasonal outbreaks is difficult. To overcome this, we reconstructed a time-series dataset that consists of cicada emergence and meteorological factors, leveraging a long-term collection of cicada...

Assessing the benefits and risks of translocations in depauperate species: a theoretical framework with an empirical validation

Elise Furlan, Bernd Gruber, Catherine Attard, Robert Wager, Adam Kerezsy, Leanne Faulks, Luciano Beheregaray & Peter Unmack
1. Conservation translocations are becoming more common to assist in the management of threatened native species. While many translocation programs focus on maximizing survival in newly established populations, consideration is also required for the persistence of source populations. 2. Here, we present and test a theoretical framework that assesses the translocation trade-off between increasing a species probability of survival and decreasing a species’ overall genetic diversity. We anticipate that i) the genetic diversity of translocated...

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  • University of Tsukuba
  • Tohoku University
  • Kyoto University
  • Zoological Research Museum Alexander Koenig
  • University of Hamburg
  • Dalhousie University
  • National Institute for Environmental Studies
  • National Institute of Genetics
  • University of the Ryukyus
  • University of Vienna