17 Works

Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation

Ming-Chih Chiu, Kei Nukazawa, Thaddeus Carvajal, Vincent Resh, Bin Li & Kozo Watanabe
Different shapes of landscape boundaries can affect the habitat networks within them and consequently the spatial genetic-patterns of a metapopulation. In this study, we used a mechanistic framework to evaluate the effects of landscape shape, through watershed elongation, on genetic divergence among populations at the metapopulation scale. Empirical genetic data from four, sympatric stream-macroinvertebrates having aerial adults were collected from streams in Japan to determine the roles of species-specific dispersal strategies on metapopulation genetics. Simulation...

Data from: Comparative tests of the species-genetic diversity correlation at neutral and non-neutral loci in four species of stream insect

Kozo Watanabe & Michael T. Monaghan
A fundamental question linking population genetics and community ecology is how adaptive processes (e.g., natural selection) and neutral processes (e.g., drift-migration equilibrium) underpin the species-genetic diversity correlation (SGDC). Here we combine genome scans and outlier loci detection with community analysis to separately test for neutral and non-neutral SGDCs in four species of stream insect. We sampled 60 localities in Japan and examined the relationships among population AFLP band richness (Br), taxon richness of the total...

Data from: Effects of 4-Hydroxy-2,3,3',4',5-pentachlorobiphenyl (4-OH-CB107) on liver transcriptome in rats: implication in the disruption of circadian rhythm and fatty acid metabolism

Mari Ochiai, Midori Iida, Tetsuro Agusa, Kohki Takaguchi, Satoshi Fujii, Kei Nomiyama & Hisato Iwata
Polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) have been detected in tissues of both wild animals and humans. Several previous studies have suggested adverse effects of OH-PCBs on the endocrine and nervous systems in mammals. However, there have been no studies on transcriptome analysis of the effects of OH-PCBs, and thus, the whole picture and mechanisms underlying the adverse effects induced by OH-PCBs are still poorly understood. We therefore investigated the mRNA expression profile...

Data from: Adaptive genetic divergence along narrow environmental gradients in four stream insects

Kozo Watanabe, So Kazama, Tatsuo Omura & Michael T. Monaghan
A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified...

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: Machine learning based detection of adaptive divergence of the stream mayfly Ephemera strigata populations

Bin Li, Sakiko Yaegashi, Thaddeus M. Carvajal, Maribet Gamboa, Ming-Chih Chiu, Zongming Ren & Kozo Watanabe
Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology is how spatial environmental heterogeneity can lead to adaptive divergence among local populations within a species. In this study, using a genome scan approach to detect candidate loci under selection, we examined adaptive divergence of the stream mayfly Ephemera strigata in the Natori River Basin in north eastern Japan. We applied a new machine...

Stan code from: Branching networks can have opposing influences on genetic variation in riverine metapopulations

Ming-Chih Chiu, Bin Li, Kei Nukazawa, Vincent Resh, Thaddeus Carvajal & Kozo Watanabe
Aim: Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in...

Data from: Early origin of sweet perception in the songbird radiation

Yasuka Toda, Meng-Ching Ko, Qiaoyi Liang, Eliot Miller, Alejandro Rico-Guevara, Tomoya Nakagita, Ayano Sakakibara, Kana Uemura, Timothy Sackton, Takashi Hayakawa, Simon Yung Wa Sin, Yoshiro Ishimaru, Takumi Misaka, Pablo Oteiza, James Crall, Scott Edwards, Shuichi Matsumura & Maude Baldwin
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large radiation containing nearly half of all living birds. We demonstrate...

Data from: A newly recognised species that has been confused with the global polyphagous pest scale insect, Coccus hesperidum Linnaeus (Hemiptera: Coccomorpha: Coccidae)

Yen-Po Lin, Hirotaka Tanaka, Takumasa Kondo & Lyn G. Cook
Coccus hesperidum L. (Hemiptera: Coccomorpha: Coccidae), the type species of the soft scale genus Coccus L., the family Coccidae and the whole of the scale insects (Coccoidea), is a cosmopolitan plant pest. Using DNA sequence data and morphological comparisons, we determine that there is a distinct species that is morphologically very similar to C. hesperidum. Here, we describe the species as Coccus praetermissus Lin & Tanaka sp. n., based on adult female specimens from Australia,...

Data from: Naturally acquired antibody responses to more than 300 Plasmodium vivax proteins in three geographic regions

Rhea J. Longley, Michael T. White, Eizo Takashima, Masayuki Morita, Bernard N. Kanoi, Connie S. N. Li Wai Suen, Inoni Betuela, Andrea Kuehn, Piyarat Sripoorote, Camila T. Franca, Peter Siba, Leanne J. Robinson, Marcus Lacerda, Jetsumon Sattabongkot, Takafumi Tsuboi & Ivo Mueller
Plasmodium vivax remains an important cause of malaria in South America and the Asia-Pacific. Naturally acquired antibody responses against multiple P. vivax proteins have been described in numerous countries, however, direct comparison of these responses has been difficult with different methodologies employed. We measured antibody responses against 307 P. vivax proteins at the time of P. vivax infection, and at 2–3 later time-points in three countries. We observed that seropositivity rates at the time of...

Data from: Trophic niche breadth of pond zooplankton species using stable isotope analysis and the relationship with the abiotic and biotic factors

Hideyuki Doi, Kwang-Hyeon Chang & Shin-Ichi Nakano
1. Zooplankton species have different feeding habits, but the diversity of their food resources and the factors governing them are still largely unknown. We here estimated the differences in the trophic niche breadths of dominant zooplankton species in ponds, using stable isotopes. 2. To understand the differences in trophic niches of different zooplankton species, we measured the carbon and nitrogen stable isotope ratios and calculated the nearest neighbor distance (NND), and standard deviation of NND...

Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia

Masato Ohtani, Toshiaki Kondo, Naoki Tani, Saneyoshi Ueno, Soon-Leong Lee, Kevin Kit Siong Ng, Norwati Muhammad, Reiner Finkeldey, Mohamad Na'iem, Sapto Indrioko, Koichi Kamiya, Ko Harada, Bibian Diway, Eyen Khoo, Kensuke Kawamura, Yoshihiko Tsumura & Leong S. Lee
Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear...

Data from: Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago

Maribet Gamboa, David Muranyi, Shota Kanmori & Kozo Watanabe
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We...

Data from: Maternally transmitted non-bacterial male killer in Drosophila biauraria

Daisuke Kageyama, Kanamu Yoshimura, Takafumi N. Sugimoto, Takehiro K. Katoh & Masayoshi Watada
A maternally inherited, all-female trait is widely found among arthropods, which is caused by bacterial endosymbionts such as Wolbachia, Rickettsia, Spiroplasma and Cardinium We discovered a single female of Drosophila biauraria, collected from Tomakomai, Hokkaido, Japan, that produced all-female offspring. This all-female trait was maternally inherited in the iso-female line (SP12F) by backcrossing with males of a normal line (SP11-20) with a 1:1 sex ratio derived from the same population. The all-female trait was not...

Data from: Magnitude and direction of stream-forest community interactions change with time scale

Amy Marcarelli, Colden Baxter, Joseph Benjamin, Yo Miyake, Masashi Murakami, Kurt Fausch & Shigeru Nakano
Networks of direct and indirect biotic interactions underpin the complex dynamics and stability of ecological systems, yet experimental and theoretical studies often yield conflicting evidence regarding the direction (positive or negative) or magnitude of these interactions. We revisited pioneering datasets collected at the deciduous forested Horonai Stream and conducted ecosystem-level syntheses to demonstrate that the direction of direct and indirect interactions can change depending on the timescale of observation. Prior experimental studies showed that terrestrial...

Data from: Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

Nikolaus U. Szucsich, Daniela Bartel, Alexander Blanke, Alexander Böhm, Alexander Donath, Makiko Fukui, Simon Grove, Shanlin Liu, Oliver Macek, Ryuichiro Machida, Bernhard Misof, Yasutaka Nakagaki, Lars Podsiadlowski, Kaoru Sekiya, Shigekazu Tomizuka, Björn M. Von Reumont, Robert M. Waterhouse, Manfred Walzl, Guanliang Meng, Xin Zhou, Günther Pass & Karen Meusemann
Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling...

Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

William Conner, Emily Delaney, Michael Bronski, Paul Ginsberg, Timothy Wheeler, Kelly Richardson, Brooke Peckenpaugh, Kevin Kim, Masayoshi Watada, Ary Hoffmann, Michael Eisen, Artyom Kopp, Brandon Cooper & Michael Turelli
The Drosophila montium species group is a clade of 94 named species closely related to the model D. melanogaster species group. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times...

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