38 Works

Data from: Shifting baselines on a tropical forest frontier: extirpations drive declines in local ecological knowledge

Zhong Kai, Teoh Shu Woan, Li Jie, Eben Goodale, Kaoru Kitajima, Robert Bagchi, Rhett D. Harrison & Zhang Kai
The value of local ecological knowledge (LEK) to conservation is increasingly recognised, but LEK is being rapidly lost as indigenous livelihoods change. Biodiversity loss is also a driver of the loss of LEK, but quantitative study is lacking. In our study landscape in SW China, a large proportion of species have been extirpated. Hence, we were interested to understand whether species extirpation might have led to an erosion of LEK and the implications this might...

Data from: Multilocus phylogeny and revised classification for mountain dragons of the genus Japalura s.l. (Reptilia: Agamidae: Draconinae) from Asia

Kai Wang, Jing Che, Simin Lin, V. Deepak, Datta-Roy Aniruddha, Ke Jiang, Jieqiong Jin, Hongman Chen & Cameron D. Siler
Although the genus Japalura s.l. has long been recognized as paraphyletic based on limited genetic sampling, its problematic taxonomy has not been revised, and phylogenetic relationships among the majority of congeners remain unknown. Here we utilize a densely sampled dataset of both multilocus genetic and morphological data to provide the first phylogenetic inference of relationships among Japalura s.l.species. Our results show that Japalura s.l. is paraphyletic, consisting of four major clades that are scattered across...

Data from: Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

Douglas W. Yu, Yinqiu Ji, Brent C. Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang & Zhaoli Ding
1) Traditional biodiversity assessment is costly in time, money, and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2) We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing, and bioinformatic analysis, which together...

Data from: PyroClean: Denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation

Ricardo Ramirez-Gonzalez, Douglas W. Yu, Catharine Bruce, Darren Heavens, Mario Caccamo & Brent C. Emerson
DatasetsThis .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript.

Data from: Assessing models of speciation under different biogeographic scenarios; an empirical study using multi-locus and RNA-seq analyses

Taylor Edwards, Marc Tollis, PingHsun Hsieh, Ryan N. Gutenkunst, Zhen Liu, Kenro Kusumi, Melanie Culver & Robert W. Murphy
Evolutionary biology often seeks to decipher the drivers of speciation, and much debate persists over the relative importance of isolation and gene flow in the formation of new species. Genetic studies of closely related species can assess if gene flow was present during speciation, because signatures of past introgression often persist in the genome. We test hypotheses on which mechanisms of speciation drove diversity among three distinct lineages of desert tortoise in the genus Gopherus....

Data from: Climate niche differentiation between two passerines despite ongoing gene flow

Shou-Hsien Li, Pei-Jen L. Shaner, Tzu-Hsuan Tsao, Rong-Chien Lin, Wei Liang, Chia-Fen Yeh, Xiao-Jun Yang, Fu-Min Lei, Fang Zhou, Can-Chao Yang & Yu-Cheng Hsu
Niche evolution underpins the generation and maintenance of biological diversity, but niche conservatism, in which niches remain little changed over time in closely related taxa and the role of ecology in niche evolution are continually debated. To test whether climate niches are conserved in two closely related passerines in East Asia – the vinous-throated (Paradoxornis webbianus) and ashy-throated (P. alphonsianus) parrotbills – we established their potential allopatric and sympatric regions using ecological niche models and...

Data from: Molecular evolution of the nuclear factor (erythroid-derived 2)-like 2 gene Nrf2 in Old World fruit bats (Chiroptera: Pteropodidae)

Qiuyuan Yin, Lei Zhu, Di Liu, David M. Irwin, Shuyi Zhang & Yi-Hsuan Pan
Mammals developed antioxidant systems to defend against oxidative damage in their daily life. Enzymatic antioxidants and low molecular weight antioxidants (LMWAs) constitute major parts of the antioxidant systems. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2, encoded by the Nrf2 gene) is a central transcriptional regulator, regulating transcription, of many antioxidant enzymes. Frugivorous bats eat large amounts of fruits that contain high levels of LMWAs such as vitamin C, thus, a reliance on LMWAs might greatly reduce...

Data from: Complex longitudinal diversification across South China and Vietnam in Stejneger's pit viper, Viridovipera stejnegeri (Schmidt, 1925) (Reptilia: Serpentes: Viperidae)

Peng Guo, Qin Liu, Fei Zhu, Guang H. Zhong, Xin Chen, Edward A. Myers, Jing Che, Liang Zhang, Thomas Ziegler, Truong Q. Nguyen & Frank T. Burbrink
Viridovipera stejnegeri is one of the most common pit vipers in Asia, with a wide distribution in southern China and Vietnam. We investigated historical demography and explored how the environment and climatic factors have shaped genetic diversity and the evolutionary history of this venomous snake. A total of 171 samples from 47 localities were sequenced and analysed for two mitochondrial gene fragments and three nuclear genes. Gene trees reveal the existence of two well-supported clades...

Data from: Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean

Zhi-Yong Yuan, Bao-Lin Zhang, Christopher J. Raxworthy, David W. Weisrock, Paul M. Hime, Jie-Qiong Jin, Emily M. Lemmon, Alan R. Lemmon, Sean D. Holland, Michelle L. Kortyna, Wei-Wei Zhou, Min-Sheng Peng, Jing Che & Elizabeth Prendini
Natatanura raw assembled sequencesNatatanura_seqs.zip

Data from: Understanding cryptic introgression and mixed ancestry of Red Junglefowl in India

Mukesh Thakur, Merwyn Fernandes, Sambandam Sathyakumar, Sujeet K. Singh, Ramesh Kumar Vijh, Jianlin Han, Dong-Dong Wu & Ya-Ping Zhang
Red Junglefowl (RJF), the wild progenitor of modern day chicken (DC), are believed to be in genetic endangerment due to introgression of domestic genes through opportunistic matings with domestic or feral chickens. Previous studies from India reported rare hybridization of RJF in wild, however, RJF population structure,pattern of gene flow and their admixture with DC populations are poorly understood at the landscape level. We conducted this study with the large sample size, covering the predicted...

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)

Björn Stelbrink, Romy Richter, Frank Köhler, Frank Riedel, Ellen Strong, Bert Van Bocxlaer, Christian Albrecht, Torsten Hauffe, Timothy Page, David Aldridge, Arthur Bogan, Li-Na Du, Marivene Manuel-Santos, Ristiyanti Marwoto, Alena Shirokaya & Thomas Von Rintelen
The Viviparidae, commonly known as River Snails, is a dominant group of freshwater snails with a nearly worldwide distribution that reaches its highest taxonomic and morphological diversity in Southeast Asia. The rich fossil record is indicative of a probable Middle Jurassic origin on the Laurasian supercontinent where the group started to diversify during the Cretaceous. However, it remains uncertain when and how the biodiversity hotspot in Southeast Asia was formed. Here, we used a comprehensive...

Data from: Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

Li Gong, Guangyi Fan, Yandong Ren, Yongjiu Chen, Liqin Liu, Qiang Qiu, Yanli Qin, Bing-Jian Liu, Lihua Jiang, Haorong Li, Yan Zeng, Qionghua Gao, Chen Zhang, Zhongkai Wang, Hui Jiang, Jinfu Tian, He Zhang, Xin Liu, Xun Xu, Wen Wang, Zhenming Lv, Yongxin Li, Bingjian Liu & Zhenming Lü
Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods living fossil species which have existed on the earth for 500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome-level T. tridentatus genome, and proofed that this genome is of very high quality with contig N50 1.69 Mb. By comparison with other arthropods, some gene families of T. tridentatus experienced significant expansion, whichare...

Data from: Systematics and macroevolution of extant and fossil scalopine moles (Mammalia, Talpidae)

Achim H. Schwermann, Kai He, Benjamin J. Peters, Thorsten Plogschties & Gabriele Sansalone
Scalopini is one of the two fully fossorial mole tribes in the family Talpidae, with remarkable adaptations to subterranean lifestyles. Most living Scalopini species are distributed in North America while a sole species occurs in China. On the other hand, scalopine fossils are found in both Eurasia and North America from upper Oligocene strata onwards, implying a complex biogeographical history. The systematic relationships of both extant and fossil Scalopini across North America and Eurasia are...

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