Assembling an illustrated family-level tree of life for exploration in mobile devices

IF 3.7 1区 生物学 Q1 Agricultural and Biological Sciences Journal of Systematics and Evolution Pub Date : 2024-02-01 DOI:10.1111/jse.13053
Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García
{"title":"Assembling an illustrated family-level tree of life for exploration in mobile devices","authors":"Andrés A. Del Risco, Diego A. Chacón, Lucia Ángel, David A. García","doi":"10.1111/jse.13053","DOIUrl":null,"url":null,"abstract":"Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.","PeriodicalId":17087,"journal":{"name":"Journal of Systematics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Systematics and Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/jse.13053","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0

Abstract

Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.

Abstract Image

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
组装图文并茂的家族级生命树,以便在移动设备中进行探索
自从大约 150 年前提出生命树的概念以来,科学界相当一部分人一直致力于生命树的重建工作,在过去二十年里,随着 DNA 序列的出现,这一工作取得了显著进展。然而,由于两个主要障碍,组建一个全面的、可探索的生命树一直是一项难以完成的任务:(i) 信息分散在多个单独的信息源中;(ii) 需要实用的可视化工具来探索大型生命树。为了克服这两个挑战,我们汇编了 1400 多项已发表的系统发育研究,并根据一套客观标准选择了代表迄今为止最佳系统发育假说的源树,旨在合成一棵科级生命树。此外,我们还利用公开发表的 5000 多个类群的序列进行了 550 多次校准,并结合化石记录中 2800 多个类群的年龄范围,确定了生命树的年代。此外,我们还为智能手机开发了一个移动应用程序,以方便对生成的树进行可视化和探索。互动功能包括通过触摸屏的缩放和平移手势进行探索、折叠分支、将特定支系可视化为子树、搜索引擎以及确定灭绝和分化日期的时间刻度等。终端还显示了生物的小插图,以更好地展示生命形态的多样性。我们的组合树目前包括 7000 多个科,其内容将通过定期更新扩展到涵盖地球上所有科一级的生命。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
Journal of Systematics and Evolution
Journal of Systematics and Evolution Agricultural and Biological Sciences-Ecology, Evolution, Behavior and Systematics
CiteScore
7.40
自引率
8.10%
发文量
1368
审稿时长
6-12 weeks
期刊介绍: Journal of Systematics and Evolution (JSE, since 2008; formerly Acta Phytotaxonomica Sinica) is a plant-based international journal newly dedicated to the description and understanding of the biological diversity. It covers: description of new taxa, monographic revision, phylogenetics, molecular evolution and genome evolution, evolutionary developmental biology, evolutionary ecology, population biology, conservation biology, biogeography, paleobiology, evolutionary theories, and related subjects.
期刊最新文献
A new stem‐group mantispoid lineage (Insecta: Neuroptera) equipped with unique raptorial structures from the Middle Jurassic of China Geographic patterns and climatic drivers of phylogenetic structure of liverworts along a long elevational gradient in the central Himalaya Phylogenetic diversity and interspecies competition shaped species diversity in adaptive radiated Ligustrum (Oleaceae) Cenozoic Ampelopsis and Nekemias leaves (Vitaceae, Ampelopsideae) from Eurasia: Paleobiogeographic and paleoclimatic implications A phylogenomic approach to disentangling the evolution of the large and diverse daisy tribe Anthemideae (Asteraceae)
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1