59 Works

Plant dispersal strategies of high tropical alpine communities across the Andes

Carolina Tovar, Inga Melcher, Buntarou Kusumoto, Francisco Cuesta, Antoine Cleef, Rosa Isela Meneses, Stephan Halloy, Luis Daniel Llambi, Stephan Beck, Priscilla Muriel, Ricardo Jaramillo, Jorge Jacome & Julieta Carilla
• Dispersal is a key ecological process that influences plant community assembly. Therefore, understanding whether dispersal strategies are associated with climate is of utmost importance, particularly in areas greatly exposed to climate change. We examined alpine plant communities located in the mountain summits of the tropical Andes across a 4000 km latitudinal gradient. We investigated species dispersal strategies and tested their association with climatic conditions and their evolutionary history. • We used dispersal-related traits (dispersal...

Earth and life evolve together from something ancestral — reply to Britz et al

Kazunori Yamahira, Shingo Fujimoto & Yasuoki Takami
Ricefishes of the family Adrianichthyidae are considered to have dispersed eastward “out-of-India” after the collision of the Indian subcontinent with Eurasia and subsequently diversified in Southeast-East Asia. In this study, we reconstructed ancestral areas of Adrianichthyidae with BioGeoBEARS, expanding the scope to include Cyprinodontiformes, the outgroup of Beloniformes to which Adrianichthyidae belongs. The results again supported the “out-of-India” dispersal scenario. The dataset contained all files necessary for the BioGeoBEARS analysis.

Species divergence and repeated ancient hybridization in a Sulawesian lake system

Kazunori Yamahira, Ixchel Mandagi, Ryo Kakioka, Javier Montenegro, Hirozumi Kobayashi, Kawilarang Masengi, Nobuyuki Inomata, Atsushi Nagano, Atsushi Toyoda, Satoshi Ansai, Masatoshi Matsunami, Ryosuke Kimura, Jun Kitano & Junko Kusumi
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent, and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes;...

Dataset for estimation of the biotic and climatic niche breadths and geographic range size of beech (Fagus) species worldwide

Qiong Cai, Erik Welk, Chengjun Ji, Wenjing Fang, Francesco Maria Sabatini, Jianxiao Zhu, Jiangling Zhu, Zhiyao Tang, Fabio Attorre, Juan Antonio Campos, Andraž Čarni, Milan Chytrý, Süleyman Çoban, Jürgen Dengler, Jiri Dolezal, Richard Field, József Pál Frink, Hamid Gholizadeh, Adrian Indreica, Ute Jandt, Dirk Nikolaus Karger, Jonathan Lenoir, Robert K. Peet, Remigiusz Pielech, Michele De Sanctis … & Helge Bruelheide
This dataset could be used to test whether the commonly observed positive range size–niche breadth relationship, as posited by the “niche breadth hypothesis”, exists for Fagus, one of the most dominant and widespread broad‐leaved deciduous tree genera in temperate forests of the Northern Hemisphere. There are many ways to estimate niche breadth. Here, we estimated biotic and climatic niche breadths per species using plot‐based co‐occurrence data and climate data, respectively. The range sizes of the...

Solving the coral species delimitation conundrum

Catalina Ramírez-Portilla, Andrew Baird, Peter Cowman, Andrea Quattrini, Saki Harii, Frederic Sinniger & Jean-François Flot
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for...

Data from: The Arabidopsis arc5 and arc6 mutations differentially affect plastid morphology in pavement and guard cells in the leaf epidermis

Makoto T. Fujiwara, Mana Yasuzawa, Kei H. Kojo, Yasuo Niwa, Tomoko Abe, Shigeo Yoshida, Takeshi Nakano & Ryuuichi D. Itoh
Chloroplasts, or photosynthetic plastids, multiply by binary fission, forming a homogeneous population in plant cells. In Arabidopsis thaliana, the division apparatus (or division ring) of mesophyll chloroplasts includes an inner envelope transmembrane protein ARC6, a cytoplasmic dynamin-related protein ARC5 (DRP5B), and members of the FtsZ1 and FtsZ2 families of proteins, which co-assemble in the stromal mid-plastid division ring (FtsZ ring). FtsZ ring placement is controlled by several proteins, including a stromal factor MinE (AtMinE1). During...

Data from: Non-nest mate discrimination and clonal colony structure in the parthenogenetic ant Cerapachys biroi

Daniel J. C. Kronauer, Kazuki Tsuji, Naomi E. Pierce & Laurent Keller
Understanding the interplay between cooperation and conflict in social groups is a major goal of biology. One important factor is genetic relatedness, and animal societies are usually composed of related but genetically different individuals, setting the stage for conflicts over reproductive allocation. Recently, however, it has been found that several ant species reproduce predominantly asexually. Although this can potentially give rise to clonal societies, in the few well-studied cases, colonies are often chimeric assemblies of...

Data from: Young giant water bug nymphs prefer larger prey: changes in foraging behavior with nymphal growth in Kirkaldyia deyrolli

Shin-Ya Ohba & Haruki Tatsuta
Raptorial characteristics may evolve in predators because of their importance in obtaining food. The giant water bug, Kirkaldyia deyrolli, possesses a claw on the terminal segment of the raptorial foreleg that is crucial for capturing prey. Claw curvature has been previously shown to change during growth in this species, but the adaptive significance of this change has not yet been explored. Predation experiments have demonstrated that young nymphs with highly curved claws caught proportionally larger...

Data from: Genomic-wide displacement and shift of the hybrid zone in the Japanese fire-bellied newt

Atsushi Tominaga, Masafumi Matsui, Natsuhiko Yoshikawa, Koshiro Eto & Kanto Nishikawa
Hybridizations on a secondary contact zone between 2 diverged lineages can have various evolutionary consequences, including the genetic replacement of one lineage by another. We detected such a case between 2 lineages (the Central and Western lineages) of the Japanese fire-bellied newt, Cynops pyrrhogaster in the Chugoku district of western Japan. We genotyped 269 individuals from 30 localities using the mitochondrial cytochrome b gene and 11 microsatellite loci. The mitochondrial DNA (mtDNA) analysis revealed that...

Data from: Territorial males can sire more offspring in nests with smaller doors in the cichlid Lamprologus lemairii

Kazutaka Ota, Satoshi Awata, Masaya Morita, Ryota Yokoyama & Masanori Kohda
To examine how territorial males counter reproductive parasites, we examined the paternity of broods guarded by territorial males using 5 microsatellite loci and factors that determine siring success in a wild population of the Lake Tanganyika cichlid Lamprologus lemairii. Females enter rock holes (nests) and spawn inside, and territorial males release milt over the nest openings. Sneakers attempt to dart into the nests, but territorial males often interrupt the attempt. The body size of territorial...

Data from: Floral traits of mammal-pollinated Mucuna macrocarpa (Fabaceae): implications for generalist-like pollination systems

Shun Kobayashi, Tetsuo Denda, Chi-Cheng Liao, Yu-Hsiu Lin, Shu-Hui Wu & Masako Izawa
Floral traits are adapted by plants to attract pollinators. Some of those plants that have different pollinators in different regions adapt to each pollinator in each region to maximize their pollination success. Mucuna macrocarpa (Fabaceae) limits the pollinators using its floral structure and is pollinated by different mammals in different regions. Here, we examine the relationships between floral traits of M. macrocarpa and the external morphology of mammalian pollinators in different regions of its distribution....

Diversity of sex chromosomes in Sulawesian medaka fishes

Satoshi Ansai, Javier Montenegro, Kawilarang W. A. Masengi, Atsushi J. Nagano, Kazunori Yamahira & Jun Kitano
Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species...

Distinct decision-making properties underlying the species specificity of group formation of flies

Riku Shirasaki, Ryoya Tanaka, Hiroki Takekata, Takashi Shimada, Yuki Ishikawa & Azusa Kamikouchi
Many animal species form groups. Group characteristics differ between species, suggesting that the decision-making of individuals for grouping varies across species. However, the actual decision-making properties that lead to interspecific differences in group characteristics remain unclear. Here, we compared the group formation processes of two Drosophilinae fly species, Colocasiomyia alocasiae and Drosophila melanogaster, which form dense and sparse groups, respectively. A high-throughput tracking system revealed that C. alocasiae flies formed groups faster than D. melanogaster...

Data from: Convergent evolution of body color between sympatric freshwater fishes via different visual sensory evolution

Javier Montenegro, Koji Mochida, Kumi Matsui, Daniel F. Mokodongan, Bayu K. A. Sumarto, Sjamsu A. Lawelle, Andy B. Nofrianto, Renny K. Hadiaty, Kawilarang W. A. Masengi, Lengxob Yong, Nobuyuki Inomata, Takahiro Irie, Yasuyuki Hashiguchi, Yohey Terai, Jun Kitano & Kazunori Yamahira
Although there are many examples of color evolution potentially driven by sensory drive, only few studies have examined whether distinct species inhabiting the same environments evolve similar body colors via shared sensory mechanisms. In this study, we tested whether two sympatric freshwater fish taxa, halfbeaks of the genus Nomorhamphus and ricefishes of the genus Oryzias in Sulawesi Island, converge in both body color and visual sensitivity. After reconstructing the phylogeny separately for Nomorhamphus and Oryzias...

Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)

Kazuki Kurita & Mamoru Toda
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA (mtDNA) indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably...

Data from: Increased local retention of reef coral larvae as a result of ocean warming

Joana Figueiredo, Andrew H. Baird, Saki Harii & Sean R. Connolly
Climate change will alter many aspects of the ecology of organisms, including dispersal patterns and population connectivity. Understanding these changes is essential to predict future species distributions, estimate potential for adaptation, and design effective networks of protected areas. In marine environments, dispersal is often accomplished by larvae. At higher temperatures, larvae develop faster, but suffer higher mortality, making the effect of temperature on dispersal difficult to predict. Here, we experimentally calibrate the effect of temperature...

Data from: Early rehabilitation to prevent post-intensive care syndrome in critically ill patients: a systematic review and meta-analysis

Yutaka Kondo, Ryota Fuke, Toru Hifumi, Junji Hatakeyama, Tetsuhiro Takei, Kazuma Yamakawa, Shigeaki Inoue & Osamu Nishida
Introduction: We examined the effectiveness of early rehabilitation for the prevention of post-intensive care syndrome (PICS), characterised by an impaired physical, cognitive, or mental health status, among survivors of critical illness. Methods: We performed a systematic literature search of several databases (Medline, Embase, and Cochrane Central Register of Controlled Trials) and a manual search to identify randomised controlled trials (RCTs) comparing the effectiveness of early rehabilitation versus no early rehabilitation or standard care for the...

Investigating sources of conflict in deep phylogenomics of vetigastropod snails

Tauana Cunha, James Reimer & Gonzalo Giribet
Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 million years ago, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity...

Mantel and partial Mantel test data and scripts of mimetic evolution of Papilio polytes in the Ryukyu Islands, Japan

Yukuto Sato, Haruki Tatsuta, Kaori Tsurui-Sato & Kazuki Tsuji
Batesian mimicry is a striking example of Darwinian evolution, and the swallowtail butterfly Papilio polytes exhibits Batesian mimicry polymorphism. These P. polytes populations show various mimic ratios among the Ryukyu Islands in Japan. We conducted Mantel and partial Mantel tests regarding the possible relationship among the mimic ratio differences, geographic distances, and average genetic distances among five islands of the Ryukyus based on 259 single nucleotide polymorphisms (SNPs) from 93 individuals.

Data from: Ecosystem size predicts the probability of speciation in migratory freshwater fish

Yo Yamasaki, Hirohiko Takeshima, Yuichi Kano, Naoharu Oseko, Toshiyuki Suzuki, Mutsumi Nishida & Katsutoshi Watanabe
Predicting speciation is a fundamental goal of research in evolutionary ecology. The probability of speciation is often positively correlated with ecosystem size. Although the mechanisms driving this correlation are generally difficult to identify, a shared geographic and ecological context provides a suitable condition to study the mechanisms that promote speciation in large ecosystems by reducing the number of factors to be considered. Here, we determined the correlation between speciation and ecosystem size, and discussed the...

Data from: Rapid adaptive evolution of photoperiodic response during invasion and range expansion across a climatic gradient

Jennifer Urbanski, Motoyoshi Mogi, Deborah O'Donnell, Mark DeCotiis, Takako Toma & Peter Armbruster
Understanding the mechanisms of adaptation to spatiotemporal environmental variation is a fundamental goal of evolutionary biology. This issue also has important implications for anticipating biological responses to contemporary climate warming and determining the processes by which invasive species are able to spread rapidly across broad geographic ranges. Here, we compare data from a historical study of latitudinal variation in photoperiodic response among Japanese and U.S. populations of the invasive Asian tiger mosquito Aedes albopictus with...

Transient amplification enhances the persistence of tropicalising coral assemblages in marginal high latitude environments

James Cant, Katie Cook, James Reimer, Takuma Mezaki, Masako Nakamura, Cliodhna O'Flaherty, Rob Salguero-Gomez & Maria Beger
Predicting the viability of species exposed to increasing climatic stress requires an appreciation for the mechanisms underpinning the success or failure of marginal populations. Rather than traditional metrics of long-term population performance, here we illustrate that short-term (i.e., transient) demographic characteristics, including measures of resistance, recovery, and compensation, are fundamental in the poleward range expansion of hard corals, facilitating the establishment of coral populations at higher latitudes. Through the annual census of tropical and subtropical...

Data from: Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations

Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira & Jun Kitano
Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult...

Data from: Crown asymmetry in high latitude forests: disentangling the directional effects of tree competition and solar radiation

Tuomas Aakala, Ichiro Shimatani, Toshihiro Abe, Yasuhiro Kubota & Timo Kuuluvainen
Light foraging by trees is a fundamental process shaping forest communities. In heterogeneous light environments this behavior is expressed as plasticity of tree growth and the development of structural asymmetries. We studied the relative influence of neighborhood structure and directional solar radiation on horizontal asymmetry of tree crowns in late-successional high latitude (67–68°N) forests in northern Fennoscandia. We described crown asymmetries as crown vectors (i.e. horizontal vectors from stem center to crown center), which we...

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems

Joseph DiBattista, James Reimer, Michael Stat, Giovanni Masucci, Piera Biondi, Maarten De Brauwer, Shaun Wilkinson, Anthony Chariton & Michael Bunce
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine...

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  • University of the Ryukyus
  • Kyoto University
  • Sam Ratulangi University
  • Tohoku University
  • National Institute of Genetics
  • Ryukoku University
  • Kyushu University
  • University of Leeds
  • University of Tsukuba
  • Saga University