Final Report Summary - PDIVCHINA (Plant biodiversity of China in a changing world: evolution and conservation)
The mechanism underlying large-scale patterns of species richness is one of the oldest, yet unresolved questions in biology. Many hypotheses have been proposed, focusing on the effects of contemporary environment (see 1 for a review). A current challenge for ecologists is to to understand how evolutionary history, historic climate and contemporary climate collectively generate large-scale patterns of species richness (2). Phylogenetic analyses provide a macro-evolutionary approach to meet the challenge. Molecular phylogenies reflect the long-term evolutionary history of floras, providing a quantitative description of the evolutionary relationships between taxa (3, 4). Integrating data of phylogenies and species distributions could shed light on our understanding of species diversity patterns.
Severe climate and land-use changes have been predicted for 21 century. How these changes at global scale would influence species distribution is still an open question. While studies indicated significant contractions in species distributions in the past century induced by climate and land-use changes (5, 6), more evaluations and projections are needed. Moreover, the question of how to effectively conserve global biodiversity under climate and land-use changes is challenging scientists and decision-makers.
The objectives of the project are 1) to understand how evolutionary history and climate influences woody plant diversity patterns in China, 2) to evaluate the impacts of future climate change on species distributions, and 3) to identify hotspots of phylogenetic diversity and to evaluate the plant diversity conservation in China.
Objective 1: We have conducted three analyses, based on which three papers were published, one in review, and two in preparation. 1) The effects of climate on woody plant diversity in China were compared with those of biogeographical regions, which were used to represent the effects of evolutionary contingencies. The results indicated significant historical signals in the patterns of species richness after accounting for the effects of climate. Moreover, by comparing the influences of environmental and spatial processes on the spatial turnover of species composition (i.e. beta diversity), we found that the historical signal in species richness patterns increased with the decrease of species range size. Two papers based on this analysis were published in 2012 (7, 8), and one in preparation. 2) A family-level phylogeny of woody plant families and genus-level phylogenies of 70 families were compiled. Then the phylogenetic structures in the species diversity patterns of woody plants in China were analyzed. The results indicated that species are older and more basal in southeastern China. Towards north, species from young clades become increasingly dominant in the local floras. A manuscript of this analysis is now in review. 3) To explore the effects of evolutionary history on species diversity of different clades, we constructed species-level phylogenies of two woody genera with wide interests, Quercus and Rhododendron. We found that the effects of contemporary water-energy dynamics on the species diversity of the two subclades of Quercus were different, which is likely mediated by the distinct evolutionary history of the two sbuclades. Our analysis further suggests that the dramatic climatic changes in late Eocene and early Oligocene significantly enhanced the evolutionary rate of Rhododendron, leading to the high species diversity within the genus. One paper based on this analysis was published in 2013 (9), and one in preparation.
Objective 2: Two analyses have been conducted to address the second objective, and three manuscripts are in preparation. 1) We calibrated species distribution models for 7680 woody species with range sizes > 20 grid cells using current environmental conditions, and projected the future distributions based on four IPCC scenarios (i.e. A1, A2, B1, and B2). The projected impacts of future climate change on species diversity indicated intensive spatial heterogeneity: under all scenarios, central to southern China tend to lose many woody species, while the Tibetan Plateau tends to gain. Due to the dominant role of Quercus in temperate forests, we calibrated species distribution models for 58 endemic Quercus species in China, and explored the potential conservation planning of Quercus species under future climate change. Two manuscripts for this part are in preparation. 2) We evaluated the phylogenetic pattern of the impacts of climate change using the supertrees, and found that the impacts were phylogenetically conserved at family level, but not at species lavel. A manuscript of this analysis is in preparation. To confirm this finding using phylogenies with branch lengths, we constructed a supermatrix of 11 genes for 3926 woody species (34% of all) in 2012, and a species-level molecular phylogeny in 2013. Further analysis is in progress. This analysis was not proposed in the proposal.
Objective 3: Two analyses have been conducted to address Objective 3, and one manuscript is in review, and one in preparation.1) The checklist and distributions of endangered plants were compiled. Using the family- and genus-level supertrees compiled and the species-level phylogeny constructed from DNA data, we estimated the phylogenetic diversity of all and the endangered woody plants in China at relevant taxonomic levels, and identified the hotspots of phylogenetic diversity. The concordance between the hotspots of phylogenetic and species diversity varied depending on the use of different phylogenetic diversity indices. A manuscript is in preparation for this analysis. 2) The data of social-economics and ecosystem services (e.g. woody species diversity, timber, forest coverage and bamboo coverage) at county-level, and the polygons of nature reserves in China were compiled. The contribution of ecosystem services and the size of nature reserves to the livelihood in different regions in China was then evaluated. We found that forest-based poverty alleviation measures must be an integral part of broader rural development strategies. A manuscript of this analysis is currently in review.
Besides the papers and manuscripts previously mentioned, Zhiheng has another four papers and two manuscripts that are the results of collaboration during the Fellowship and are closely linked with the project. He was invited to give talks in four conferences, and four universities/institutes to present the research. Overall, scientific insight obtained from this project provides a useful knowledge-based foundation to formulate strategies for managing the future of biodiversity in light of global change in climate.
Through the project, Zhiheng received extensive training on species distribution models and bioinformatics, including dealing with mega amount of sequence data, and the state-of-the-art technologies for phylogeny reconstruction. He has also developed an R/MatLab package, which includes massive functions for bioinformatics, phylogeny construction, comparative phylogenetic analysis, and spatial/phylogenetic data visualization. This package will be helpful for future research. Moreover, in 2012, he received the prestigious “1000 Young Talent Program” in China, which is comparable to the ERC grant in Europe, and got a faculty position in Peking University in Beijing, China.
References
1. Currie DJ, et al. (2004) Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecol. Lett. 7(12):1121-1134.
2. Mittelbach GG, et al. (2007) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10:315-331.
3. Faith D (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61(1):1-10.
4. Schipper J, et al. (2008) The status of the world's land and marine mammals: diversity, threat, and knowledge. Science 322(5899):225-230.
5. Thuiller W, Lavorel S, Araújo MB, Sykes MT, & Prentice IC (2005) Climate change threats to plant diversity in Europe. Proc. Natl. Acad. Sci. U.S.A. 102(23):8245-8250.
6. Jetz W, Wilcove DS, & Dobson AP (2007) Projected impacts of climate and land-use change on the global diversity of birds. PLoS BIOLOGY 5(6):1211-1219.
7. Wang Z, Fang J, Tang Z, & Lin X (2012) Relative role of contemporary environment versus history in shaping diversity patterns of China's woody plants. Ecography 35:1124-1133.
8. Wang Z, Fang J, Tang Z, & Shi L (2012) Geographical patterns in the beta diversity of China's woody plants: The influence of space, environment, and range size. Ecography 35:1092-1102.
9. Xu X, Wang Z, Rahbek C, Lessard J-P, & Fang J (2013) Evolutionary history influences the effects of water–energy dynamics on oak diversity in Asia. J. Biogeogr.:n/a-n/a.
Severe climate and land-use changes have been predicted for 21 century. How these changes at global scale would influence species distribution is still an open question. While studies indicated significant contractions in species distributions in the past century induced by climate and land-use changes (5, 6), more evaluations and projections are needed. Moreover, the question of how to effectively conserve global biodiversity under climate and land-use changes is challenging scientists and decision-makers.
The objectives of the project are 1) to understand how evolutionary history and climate influences woody plant diversity patterns in China, 2) to evaluate the impacts of future climate change on species distributions, and 3) to identify hotspots of phylogenetic diversity and to evaluate the plant diversity conservation in China.
Objective 1: We have conducted three analyses, based on which three papers were published, one in review, and two in preparation. 1) The effects of climate on woody plant diversity in China were compared with those of biogeographical regions, which were used to represent the effects of evolutionary contingencies. The results indicated significant historical signals in the patterns of species richness after accounting for the effects of climate. Moreover, by comparing the influences of environmental and spatial processes on the spatial turnover of species composition (i.e. beta diversity), we found that the historical signal in species richness patterns increased with the decrease of species range size. Two papers based on this analysis were published in 2012 (7, 8), and one in preparation. 2) A family-level phylogeny of woody plant families and genus-level phylogenies of 70 families were compiled. Then the phylogenetic structures in the species diversity patterns of woody plants in China were analyzed. The results indicated that species are older and more basal in southeastern China. Towards north, species from young clades become increasingly dominant in the local floras. A manuscript of this analysis is now in review. 3) To explore the effects of evolutionary history on species diversity of different clades, we constructed species-level phylogenies of two woody genera with wide interests, Quercus and Rhododendron. We found that the effects of contemporary water-energy dynamics on the species diversity of the two subclades of Quercus were different, which is likely mediated by the distinct evolutionary history of the two sbuclades. Our analysis further suggests that the dramatic climatic changes in late Eocene and early Oligocene significantly enhanced the evolutionary rate of Rhododendron, leading to the high species diversity within the genus. One paper based on this analysis was published in 2013 (9), and one in preparation.
Objective 2: Two analyses have been conducted to address the second objective, and three manuscripts are in preparation. 1) We calibrated species distribution models for 7680 woody species with range sizes > 20 grid cells using current environmental conditions, and projected the future distributions based on four IPCC scenarios (i.e. A1, A2, B1, and B2). The projected impacts of future climate change on species diversity indicated intensive spatial heterogeneity: under all scenarios, central to southern China tend to lose many woody species, while the Tibetan Plateau tends to gain. Due to the dominant role of Quercus in temperate forests, we calibrated species distribution models for 58 endemic Quercus species in China, and explored the potential conservation planning of Quercus species under future climate change. Two manuscripts for this part are in preparation. 2) We evaluated the phylogenetic pattern of the impacts of climate change using the supertrees, and found that the impacts were phylogenetically conserved at family level, but not at species lavel. A manuscript of this analysis is in preparation. To confirm this finding using phylogenies with branch lengths, we constructed a supermatrix of 11 genes for 3926 woody species (34% of all) in 2012, and a species-level molecular phylogeny in 2013. Further analysis is in progress. This analysis was not proposed in the proposal.
Objective 3: Two analyses have been conducted to address Objective 3, and one manuscript is in review, and one in preparation.1) The checklist and distributions of endangered plants were compiled. Using the family- and genus-level supertrees compiled and the species-level phylogeny constructed from DNA data, we estimated the phylogenetic diversity of all and the endangered woody plants in China at relevant taxonomic levels, and identified the hotspots of phylogenetic diversity. The concordance between the hotspots of phylogenetic and species diversity varied depending on the use of different phylogenetic diversity indices. A manuscript is in preparation for this analysis. 2) The data of social-economics and ecosystem services (e.g. woody species diversity, timber, forest coverage and bamboo coverage) at county-level, and the polygons of nature reserves in China were compiled. The contribution of ecosystem services and the size of nature reserves to the livelihood in different regions in China was then evaluated. We found that forest-based poverty alleviation measures must be an integral part of broader rural development strategies. A manuscript of this analysis is currently in review.
Besides the papers and manuscripts previously mentioned, Zhiheng has another four papers and two manuscripts that are the results of collaboration during the Fellowship and are closely linked with the project. He was invited to give talks in four conferences, and four universities/institutes to present the research. Overall, scientific insight obtained from this project provides a useful knowledge-based foundation to formulate strategies for managing the future of biodiversity in light of global change in climate.
Through the project, Zhiheng received extensive training on species distribution models and bioinformatics, including dealing with mega amount of sequence data, and the state-of-the-art technologies for phylogeny reconstruction. He has also developed an R/MatLab package, which includes massive functions for bioinformatics, phylogeny construction, comparative phylogenetic analysis, and spatial/phylogenetic data visualization. This package will be helpful for future research. Moreover, in 2012, he received the prestigious “1000 Young Talent Program” in China, which is comparable to the ERC grant in Europe, and got a faculty position in Peking University in Beijing, China.
References
1. Currie DJ, et al. (2004) Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecol. Lett. 7(12):1121-1134.
2. Mittelbach GG, et al. (2007) Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10:315-331.
3. Faith D (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61(1):1-10.
4. Schipper J, et al. (2008) The status of the world's land and marine mammals: diversity, threat, and knowledge. Science 322(5899):225-230.
5. Thuiller W, Lavorel S, Araújo MB, Sykes MT, & Prentice IC (2005) Climate change threats to plant diversity in Europe. Proc. Natl. Acad. Sci. U.S.A. 102(23):8245-8250.
6. Jetz W, Wilcove DS, & Dobson AP (2007) Projected impacts of climate and land-use change on the global diversity of birds. PLoS BIOLOGY 5(6):1211-1219.
7. Wang Z, Fang J, Tang Z, & Lin X (2012) Relative role of contemporary environment versus history in shaping diversity patterns of China's woody plants. Ecography 35:1124-1133.
8. Wang Z, Fang J, Tang Z, & Shi L (2012) Geographical patterns in the beta diversity of China's woody plants: The influence of space, environment, and range size. Ecography 35:1092-1102.
9. Xu X, Wang Z, Rahbek C, Lessard J-P, & Fang J (2013) Evolutionary history influences the effects of water–energy dynamics on oak diversity in Asia. J. Biogeogr.:n/a-n/a.