Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Gene...Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Generalized Linear Models(PGLMs)address this issue by integrating phylogenetic relationships into statistical models.However,accurately partitioning explained variance among correlated predictors remains challenging.The phylolm.hp R package tackles this problem by extending the concept of“average shared variance”to PGLMs,enabling nuanced quantificationof the relative importance of phylogeny and other predictors.The package calculates individual likelihood-based R^(2) contributions of phylogeny and each predictor,accounting for both unique and shared explained variance.This approach overcomes limitations of traditional partial R^(2) methods,which often fail to sum the total R^(2) due to multicollinearity.We demonstrate the functionality of phylolm.hp through two case studies:one involving continuous trait data(maximum tree height in Californian species)and another focusing on binary trait data(species invasiveness in North American forests).The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.展开更多
二叠纪末生物大灭绝(The end-Permain mass extinction, EPME)作为全球地质历史时期最大的灭绝事件,导致了约75%的陆生物种和约81%的海生物种的灭绝,全球范围内的陆生植被、昆虫和陆地四足脊椎动物历经了快速和毁灭性的打击,显著灭绝的...二叠纪末生物大灭绝(The end-Permain mass extinction, EPME)作为全球地质历史时期最大的灭绝事件,导致了约75%的陆生物种和约81%的海生物种的灭绝,全球范围内的陆生植被、昆虫和陆地四足脊椎动物历经了快速和毁灭性的打击,显著灭绝的海洋物种包括■、三叶虫、棘皮动物和珊瑚等,大部分灭绝或者被替代的物种包括腕足类、双壳类、放射虫、有孔虫和菊石等,EPME生物灭绝具有区域性、选择性和阶段性等特点。西伯利亚大火成岩省(the Siberian large ignous province, SLIP)的爆发与EPME时间高度耦合,SLIP及其连带的一系列次生事件被认为是EPME的主要驱动力,同时也是滞缓生物复苏的主要因素。海洋缺氧、海水升温等部分次生事件的持续时间、强度和区域分布仍存争议,且单一次生事件不能独立支撑EPME,EPME是多个因素综合叠加作用的结果。SLIP爆发促使埋藏在内陆盆地和大陆架沉积物中的温室气体向大气圈大量释放,全球气候快速变暖导致陆地危机先行发生,极端干旱天气促进了森林野火的频发和陆地生态系统的崩溃;大陆风化加剧使得大量碎屑注入海洋造成严重的富营养化、海底生物缺氧、海洋酸化和海洋古生产力紊乱等,致使海洋灭绝事件的发生,陆地灭绝的滞后性导致陆地危机的结束时间晚于海洋灭绝事件。二叠纪末全球性的环境突变对地球生态系统产生了巨大的影响,通过综述EPME演变过程,深入探讨引起生物大灭绝的原因,对了解二叠纪末全球生态系统崩溃和预测今后类似地质事件的发生具有重要意义。展开更多
2009年,时逢英国博物学家查尔斯.罗伯特.达尔文(Charles Robert Darwin,1809-1882)诞辰200周年,进化论光辉著作《物种起源》发表150周年。历史的发展不断认证达尔文的《物种起源》一书是生物学史上不朽的经典著作,如今《物种起源》所提...2009年,时逢英国博物学家查尔斯.罗伯特.达尔文(Charles Robert Darwin,1809-1882)诞辰200周年,进化论光辉著作《物种起源》发表150周年。历史的发展不断认证达尔文的《物种起源》一书是生物学史上不朽的经典著作,如今《物种起源》所提及的许多观点已成为人尽皆知的常识,并且还在不断地发展、完善,为人类认识自然和自身发展指点方向。文章追忆了先贤的卓越科学贡献和科学探索精神,并对百年来科学进步和进化论的发展重要成果进行了简要的评述,指出了进化论未来研究的重点问题。展开更多
Magnetic sense,or termed magnetoreception,has evolved in a broad range of taxa within the animal kingdom to facilitate orientation and navigation.MagRs,highly conserved A-type iron-sulfur proteins,are widely distribut...Magnetic sense,or termed magnetoreception,has evolved in a broad range of taxa within the animal kingdom to facilitate orientation and navigation.MagRs,highly conserved A-type iron-sulfur proteins,are widely distributed across all phyla and play essential roles in both magnetoreception and iron-sulfur cluster biogenesis.However,the evolutionary origins and functional diversification of MagRs from their prokaryotic ancestor remain unclear.In this study,MagR sequences from 131 species,ranging from bacteria to humans,were selected for analysis,with 23 representative sequences covering species from prokaryotes to Mollusca,Arthropoda,Osteichthyes,Reptilia,Aves,and mammals chosen for protein expression and purification.Biochemical studies revealed a gradual increase in total iron content in MagRs during evolution.Three types of MagRs were identified,each with distinct iron and/or iron-sulfur cluster binding capacity and protein stability,indicating continuous expansion of the functional roles of MagRs during speciation and evolution.This evolutionary biochemical study provides valuable insights into how evolution shapes the physical and chemical properties of biological molecules such as MagRs and how these properties influence the evolutionary trajectories of MagRs.展开更多
基金supported by the National Natural Science Foundation of China(32271551,32571954)National Key Research and Development Program of China(2023YFF0805800)the Metasequoia funding of Nanjing Forestry University.
文摘Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry(phylogeny)from those of ecological or trait-based predictors on species traits.Phylogenetic Generalized Linear Models(PGLMs)address this issue by integrating phylogenetic relationships into statistical models.However,accurately partitioning explained variance among correlated predictors remains challenging.The phylolm.hp R package tackles this problem by extending the concept of“average shared variance”to PGLMs,enabling nuanced quantificationof the relative importance of phylogeny and other predictors.The package calculates individual likelihood-based R^(2) contributions of phylogeny and each predictor,accounting for both unique and shared explained variance.This approach overcomes limitations of traditional partial R^(2) methods,which often fail to sum the total R^(2) due to multicollinearity.We demonstrate the functionality of phylolm.hp through two case studies:one involving continuous trait data(maximum tree height in Californian species)and another focusing on binary trait data(species invasiveness in North American forests).The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.
文摘二叠纪末生物大灭绝(The end-Permain mass extinction, EPME)作为全球地质历史时期最大的灭绝事件,导致了约75%的陆生物种和约81%的海生物种的灭绝,全球范围内的陆生植被、昆虫和陆地四足脊椎动物历经了快速和毁灭性的打击,显著灭绝的海洋物种包括■、三叶虫、棘皮动物和珊瑚等,大部分灭绝或者被替代的物种包括腕足类、双壳类、放射虫、有孔虫和菊石等,EPME生物灭绝具有区域性、选择性和阶段性等特点。西伯利亚大火成岩省(the Siberian large ignous province, SLIP)的爆发与EPME时间高度耦合,SLIP及其连带的一系列次生事件被认为是EPME的主要驱动力,同时也是滞缓生物复苏的主要因素。海洋缺氧、海水升温等部分次生事件的持续时间、强度和区域分布仍存争议,且单一次生事件不能独立支撑EPME,EPME是多个因素综合叠加作用的结果。SLIP爆发促使埋藏在内陆盆地和大陆架沉积物中的温室气体向大气圈大量释放,全球气候快速变暖导致陆地危机先行发生,极端干旱天气促进了森林野火的频发和陆地生态系统的崩溃;大陆风化加剧使得大量碎屑注入海洋造成严重的富营养化、海底生物缺氧、海洋酸化和海洋古生产力紊乱等,致使海洋灭绝事件的发生,陆地灭绝的滞后性导致陆地危机的结束时间晚于海洋灭绝事件。二叠纪末全球性的环境突变对地球生态系统产生了巨大的影响,通过综述EPME演变过程,深入探讨引起生物大灭绝的原因,对了解二叠纪末全球生态系统崩溃和预测今后类似地质事件的发生具有重要意义。
文摘2009年,时逢英国博物学家查尔斯.罗伯特.达尔文(Charles Robert Darwin,1809-1882)诞辰200周年,进化论光辉著作《物种起源》发表150周年。历史的发展不断认证达尔文的《物种起源》一书是生物学史上不朽的经典著作,如今《物种起源》所提及的许多观点已成为人尽皆知的常识,并且还在不断地发展、完善,为人类认识自然和自身发展指点方向。文章追忆了先贤的卓越科学贡献和科学探索精神,并对百年来科学进步和进化论的发展重要成果进行了简要的评述,指出了进化论未来研究的重点问题。
基金National Natural Science Foundation of China(31640001 and T2350005 to C.X.)Ministry of Science and Technology of China(2021ZD0140300 to C.X.)Presidential Foundation of Hefei Institutes of Physical Science,Chinese Academy of Sciences(Y96XC11131,E26CCG27,and E26CCD15 to C.X.,E36CWGBR24B and E36CZG14132 to T.C.)。
文摘Magnetic sense,or termed magnetoreception,has evolved in a broad range of taxa within the animal kingdom to facilitate orientation and navigation.MagRs,highly conserved A-type iron-sulfur proteins,are widely distributed across all phyla and play essential roles in both magnetoreception and iron-sulfur cluster biogenesis.However,the evolutionary origins and functional diversification of MagRs from their prokaryotic ancestor remain unclear.In this study,MagR sequences from 131 species,ranging from bacteria to humans,were selected for analysis,with 23 representative sequences covering species from prokaryotes to Mollusca,Arthropoda,Osteichthyes,Reptilia,Aves,and mammals chosen for protein expression and purification.Biochemical studies revealed a gradual increase in total iron content in MagRs during evolution.Three types of MagRs were identified,each with distinct iron and/or iron-sulfur cluster binding capacity and protein stability,indicating continuous expansion of the functional roles of MagRs during speciation and evolution.This evolutionary biochemical study provides valuable insights into how evolution shapes the physical and chemical properties of biological molecules such as MagRs and how these properties influence the evolutionary trajectories of MagRs.
