38 Works

Data from: Smaller is better: drift in gaze measurements due to pupil dynamics

Jan Drewes, Weina Zhu, Yingzhou Hu & Xintian Hu
Camera-based eye trackers are the mainstay of eye movement research and countless practical applications of eye tracking. Recently, a significant impact of changes in pupil size on gaze position as measured by camera-based eye trackers has been reported. In an attempt to improve the understanding of the magnitude and population-wise distribution of the pupil-size dependent shift in reported gaze position, we present the first collection of binocular pupil drift measurements recorded from 39 subjects. The...

Data from: Assessing species boundaries and the phylogenetic position of the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae), using coalescent-based methods

Xin Chen, Ke Jiang, Peng Guo, Song Huang, Dingqi Rao, Li Ding, Hirohiko Takeuchi, Jing Che, Yaping Zhang, Edward A. Myers, Frank T. Burbrink & Ya-Ping Zhang
Delimiting species and clarifying phylogenetic relationships are the main goals of systematics. For species with questionable taxonomic status, species delimitation approaches using multi-species coalescent models with multiple loci are recommended if morphological data are unavailable or unhelpful. Moreover, these methods will also reduce subjectivity based on genetic distance or requirement of monophyletic genetic lineages. We determine the validity and phylogenetic position of a rare and long controversial species of Chinese reptile, the Szechwan ratsnake (Euprepiophis...

Divergent adaptations in resource-use traits explain how pikas thrive on the roof of the world

Anderson Feijo, Deyan Ge, Zhixin Wen, Lin Xia & Qisen Yang
Life in extreme environments is possible through multilevel adaptations to physical and biotic stresses. At high elevations, species face numerous challenges, besides low oxygen levels, but previous studies have focused on genetic and physiological adaptations to chronic hypoxia while overlooking other key strategies for thriving in alpine landscapes. Here, we investigate resource-use trait adaptations to extreme elevations using pikas as a model, lagomorphs distributed up to 6200 metres and reaching maximum diversity on the Qinghai-Tibet...

Data from: Plant diversity accurately predicts insect diversity in two tropical landscapes

Kai Zhang, Siliang Lin, Yinqiu Ji, Chenxue Yang, Xiaoyang Wang, Chunyan Yang, Hesheng Wang, Haisheng Jiang, Rhett D. Harrison & Douglas W. Yu
Plant diversity surely determines arthropod diversity, but only moderate correlations between arthropod and plant species richness had been observed until Basset et al. (Science, 338, 2012 and 1481) finally undertook an unprecedentedly comprehensive sampling of a tropical forest and demonstrated that plant species richness could indeed accurately predict arthropod species richness. We now require a high-throughput pipeline to operationalize this result so that we can (i) test competing explanations for tropical arthropod megadiversity, (ii) improve...

Data from: Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Torrey W. Rodgers, Charles C. Y. Xu, Jacalyn Giacalone, Karen M. Kapheim, Kristin Saltonstall, Marta Vargas, Douglas W. Yu, Panu Somervuo, W. Owen McMillan & Patrick A. Jansen
Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera-trapping. We collected 1084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For...

Biodiversity soup II

Douglas Yu, Chunyan Yang, Kristine Bohmann, Xiaoyang Wang, Cai Wang, Nathan Wales, Zhaoli Ding & Shyam Gopalakrishnan
1. Despite widespread recognition of its great promise to aid decision-making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise during PCR amplification, sequencing, and library generation. We present a co-designed wet-lab and bioinformatic workflow for metabarcoding bulk samples that removes both false-positive (tag jumps, chimeras, erroneous sequences) and false-negative (‘dropout’) errors. However, we find that it is not possible to recover relative-abundance information from amplicon data,...

Data from: Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains

Kai He, Eliécer E. Gutiérrez, Neander M. Heming, Klaus-Peter Koepfli, Tao Wan, Shuiwang He, Jin Wei, Shao-Ying Liu & Xue-Long Jiang
Biodiversity hotspots should be given high priority for conservation under the situation of global climate change. The sky islands in southwestern China are characterized by extraordinarily high species diversity and are among one of the world’s top biodiversity hotspots. However, neither the actual species diversity in this region or mechanisms generating this diversity are well explored. Here, we report on the phylogeographic analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial mammal that inhabits the...

A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak

Jin-Cheng Zhong, Qiu-Mei Ji, Jin-Wei Xin, Zhi-Xin Chai, Cheng-Fu Zhang, Yangla Dawa, Sang Luo, Qiang Zhang, Zhandui Pingcuo, Min-Sheng Peng, Yong Zhu, Han-Wen Cao, Hui Wang & Jian-Lin Han
Yak is an important livestock for the people who lived in harsh and oxygen-deprived Qinghai-Tibetan Plateau and Hindu-Kush Himalayan Mountains. Although there is a yak genome be sequenced in 2012, the assembly is quite fragmented due to the limitation of Illumina sequencing technology. An accurate and complete reference genome is critical for studying genetic variation of a specie. Long-read sequences are more complete than short-read ones, and they have been successfully used for high-quality genome...

Data from: High-throughput monitoring of wild bee diversity and abundance via mitogenomics

Min Tang, Chloe J. Hardman, Yinqiu Ji, Guanliang Meng, Shanlin Liu, Meihua Tang, Shenzhou Yang, Ellen D. Moss, Jiaxin Wang, Chenxue Yang, Catharine Bruce, Tim Nevard, Simon G. Potts, Xin Zhou, Douglas W. Yu & Meihua Tan
1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline. 2. We show that the metagenomic mining and...

Data from: Comparative phylogeography in marginal seas of the northwestern Pacific

Gang Ni, Qi Li, Lingfeng Kong & Hong Yu
The maturation of marine phylogeography depends on integration of comparative information across different regions globally. The northwestern Pacific, characterized by unique tectonic setting, however, is still underrepresented. This study seeks to highlight its phylogeographical history based on available population data, focusing on three seas: the East China Sea (ECS), the South China Sea (SCS), and the Sea of Japan (SOJ). We first conducted a literature survey to evaluate current research efforts, and then re-analysed the...

Data from: Yet another empty forest: considering the conservation value of a recently established tropical nature reserve

Rachakonder Sreekar, Kai Zhang, Jianchu Xu, Rhett D. Harrison & Rachakonda Sreekar
The primary approach used to conserve tropical biodiversity is in the establishment of protected areas. However, many tropical nature reserves are performing poorly and interventions in the broader landscape may be essential for conserving biodiversity both within reserves and at large. Between October 2010 and 2012, we conducted bird surveys in and around a recently established nature reserve in Xishuangbanna, China. We constructed a checklist of observed species, previously recorded species, and species inferred to...

Data from: Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

Panu Somervuo, Douglas W. Yu, Charles C.Y. Xu, YinQiu Ji, Jenni Hultman, Helena Wirta & Otso Ovaskainen
A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However,...

A single mutation underlying phenotypic convergence for hypoxia adaptation on the Qinghai-Tibetan Plateau

Dongming Xu
Similar highland phenotypes have evolved in different endemic mammals in the Qinghai-Tibetan Plateau (QTP). However, until' now, we know little about genomic underpinnings of these convergent phenotypes. Here, we de novo sequenced genomes of plateau pika and plateau zokor. Along with yak and Tibetan antelope genomes, we discovered that all four QTP mammal species share a mutation Q247R in RETSAT. In vitro functional experiments indicate that this mutation significantly increases RETSAT enzymatic activity. Knock-in mice...

Data from: Discriminative host sanction together with relatedness promote the cooperation in fig/fig wasp mutualism

Rui-Wu Wang, Bao-Fa Sun & Yan Yang
1. Sanctioning or punishing is regarded as one of the most important dynamics in the evolution of cooperation. However, it has not been empirically examined yet whether or not such enforcement selection by sanctioning or punishing and classical theories like kin or reciprocity selection are separate mechanisms contributing to the evolution of cooperation. In addition, it remains largely unclear what factors determine the intensity or effectiveness of sanction. 2. Here, we show that in the...

Data from: Mitochondrial genomes of domestic animals need scrutiny

Ni-Ni Shi, Long Fan, Yong-Gang Yao, Min-Sheng Peng & Ya-Ping Zhang
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that...

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)

Yunhe Wu, Fang Yan, Bryan L. Stuart, Elizabeth Prendini, Chatmongkon Suwannapoom, Hollis A. Dahn, Bao-Lin Zhang, Hong-Xia Cai, Yong-Biao Xu, Ke Jiang, Hong-Man Chen, Alan R. Lemmon, Emily Moriarty Lemmon, Christopher J. Raxworthy, Nikolai L. Orlov, Robert W. Murphy & Jing Che
Amolops is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus...

Predicting barrier effects of transportation networks on Asian elephants: Implications for environmental impact assessment

Cheng Huang, Xueyou Li, Wenqiang Hu & Xuelong Jiang
The rapid proliferation of transportation networks (TNs) is a threat to wide–ranged animals through habitat erosion, road–kill, and indirect socio–ecological interaction. In most cases, environmental impact assessments of TNs about animals are descriptive and targeted to direct impacts of the “linear features”, while indirect and cumulative impacts are relatively neglected. Using spatially explicit data of elephant–caused damage during 2012–2015 in China, we quantified barrier effects of TN on Asian elephants and predicted the effects under...

Genome, annotations and SNPs for the green peafowl and associated scripts

Feng Dong, Hao-Chih Kuo, Guo-Ling Chen, Fei Wu, Peng-Fei Shan, Jie Wang, De Chen, Chih-Ming Hung, Yang Liu & Xiao-Jun Yang
Both anthropogenic impacts and historical climate change could contribute to population decline and species extinction, but their relative importance has yet to be determined. Emerging approaches based on genomic, climatic and anthropogenic data provide a promising analytical framework to address this question. This study applied such an integrative approach to examine potential drivers for endangerment of the green peafowl (Pavo muticus). Several demographic reconstructions based on population genomes congruently retrieved a drastic population declination since...

Small mammal species richness and turnover along elevational gradient in Yulong Mountain, Yunnan, Southwest China

Zhongzheng Chen, Xueyou Li, Wenyu Song, Quan Li, Kenneth Onditi, Laxman Khanal & Xuelong Jiang
Understanding the species diversity patterns along elevational gradients is critical for biodiversity conservation in mountainous regions. We examined the elevational patterns of species richness and turnover, and evaluated the effects of spatial and environmental factors on non-volant small mammals (hereafter ‘small mammal’) predicted a priori by alternative hypotheses [Mid-domain effect (MDE), species area relationship (SAR), energy, environmental stability and habitat complexity)] proposed to explain the variation of diversity. We designed a standardized sampling scheme to...

Supplementary material of the article “Elevation patterns and critical environmental drivers of the taxonomic, functional and phylogenetic diversity of small mammals in a karst mountain area”.

Jian Sun, Zhixin Wen, Anderson Feijó, Jilong Cheng, Yanqun Wang, Song Li, Deyan Ge, Lin Xia & Qisen Yang
Understanding how biodiversity components are related under different environmental factors is a fundamental challenge for ecology studies, yet there is little knowledge of this interplay among the biotas, especially small mammals, in karst mountain areas. Here, we examine the elevation patterns of the taxonomic diversity (TD), phylogenetic diversity (PD) and functional diversity (FD) of small mammals in a karst mountain area, the Wuling Mountains, Southwest China, and compare these patterns between taxa (Rodentia and Eulipotyphla)...

Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)

Feng Dong, Fa-Sheng Zou, Fu-Min Lei, Wei Liang, Shou-Hsien Li & Xiao-Jun Yang
Species-level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. The present study aims to test the underlying causes behind the observed paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar...

Data from: Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico

Christopher Blair, Victor H. Jiménez Arcos, Fausto R. Mendez De La Cruz & Robert W. Murphy
Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity...

Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

Carmelo Andujar, Paula Arribas, Clare Gray, Katherine Bruce, Guy Woodward, Douglas W. Yu & Alfried P. Vogler
Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in...

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Jinmin Chen, Elizabeth Prendini, Yun-He Wu, Bao-Lin Zhang, Chatmongkon Suwannapoom, Hong-Man Chen, Jie-Qiong Jin, Emily Moriarty Lemmon, Alan R. Lemmon, Bryan L. Stuart, Christopher J. Raxworthy, Robert W. Murphy, Zhi-Yong Yuan & Jing Che
Rhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated...

Data from: Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Jesse F. Abrams, Lisa Hörig, Robert Brozovic, Jan Axtner, Alex Crampton-Platt, Azlan Mohamed, Seth T. Wong, Rahel Sollmann, Douglas W. Yu & Andreas Wilting
1.Invertebrate‐derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost‐efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments. 2.Here, we compare concurrent iDNA and camera‐trap surveys. Leeches were repeatedly collected in close vicinity to 64...

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