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The Sinocyclocheilus cavefish genome provides insights into cave adaptation

Overview of attention for article published in BMC Biology, January 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (95th percentile)
  • High Attention Score compared to outputs of the same age and source (88th percentile)

Mentioned by

news
2 news outlets
blogs
2 blogs
twitter
8 tweeters
facebook
1 Facebook page

Citations

dimensions_citation
180 Dimensions

Readers on

mendeley
130 Mendeley
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Title
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Published in
BMC Biology, January 2016
DOI 10.1186/s12915-015-0223-4
Pubmed ID
Authors

Junxing Yang, Xiaoli Chen, Jie Bai, Dongming Fang, Ying Qiu, Wansheng Jiang, Hui Yuan, Chao Bian, Jiang Lu, Shiyang He, Xiaofu Pan, Yaolei Zhang, Xiaoai Wang, Xinxin You, Yongsi Wang, Ying Sun, Danqing Mao, Yong Liu, Guangyi Fan, He Zhang, Xiaoyong Chen, Xinhui Zhang, Lanping Zheng, Jintu Wang, Le Cheng, Jieming Chen, Zhiqiang Ruan, Jia Li, Hui Yu, Chao Peng, Xingyu Ma, Junmin Xu, You He, Zhengfeng Xu, Pao Xu, Jian Wang, Huanming Yang, Jun Wang, Tony Whitten, Xun Xu, Qiong Shi

Abstract

An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

Twitter Demographics

The data shown below were collected from the profiles of 8 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 130 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Portugal 1 <1%
Unknown 128 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 26 20%
Researcher 19 15%
Student > Master 18 14%
Other 8 6%
Student > Bachelor 8 6%
Other 22 17%
Unknown 29 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 47 36%
Biochemistry, Genetics and Molecular Biology 26 20%
Environmental Science 6 5%
Engineering 3 2%
Unspecified 2 2%
Other 10 8%
Unknown 36 28%

Attention Score in Context

This research output has an Altmetric Attention Score of 35. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 15 February 2021.
All research outputs
#972,266
of 22,837,982 outputs
Outputs from BMC Biology
#249
of 1,997 outputs
Outputs of similar age
#18,725
of 393,289 outputs
Outputs of similar age from BMC Biology
#3
of 25 outputs
Altmetric has tracked 22,837,982 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,997 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 21.5. This one has done well, scoring higher than 87% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 393,289 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 95% of its contemporaries.
We're also able to compare this research output to 25 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 88% of its contemporaries.