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Oliveira EVDS, Landim MF, Gouveia SF. Assembly structures of coastal woody species of eastern South America: Patterns and drivers. PLANT DIVERSITY 2024; 46:611-620. [PMID: 39290883 PMCID: PMC11403147 DOI: 10.1016/j.pld.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 09/19/2024]
Abstract
Tropical regions have provided new insights into how ecological communities are assembled. In dry coastal communities, water stress has been hypothesized to determine plant assembly structure by favoring preadapted lineages from neighboring ecosystems, consistent with functional clustering. However, it is unclear whether this hypothesis is sufficient to explain how coastal communities in tropical ecosystems are assembled. Here, we test whether water stress or other factors drive community assembly in woody plant communities across the coastal zone of Brazil, a tropical ecosystem. We characterized functional and phylogenetic structures of these communities and determined the underlying environmental factors (e.g., water stress, historical climate stability, edaphic constraints, and habitat heterogeneity) that drive their community assembly. Assemblages of coastal woody species show geographically varied patterns, including stochastic arrangements, clustering, and overdispersion of species relative to their traits and phylogenetic relatedness. Topographic complexity, water vapor pressure, and soil nutrient availability best explained the gradient in the functional structure. Water deficit, water vapor pressure, and soil organic carbon were the best predictors of variation in phylogenetic structure. Our results support the water-stress conservatism hypothesis on functional and phylogenetic structure, as well as the effect of habitat heterogeneity on functional structure and edaphic constraints on functional and phylogenetic structure. These effects are associated with increased phenotypic and phylogenetic divergence of woody plant assemblages, which is likely mediated by abiotic filtering and niche opportunities, suggesting a complex pattern of ecological assembly.
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Affiliation(s)
- Eduardo Vinícius da Silva Oliveira
- Graduate Program in Ecology and Conservation, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- National Institute of Science and Technology Ecology, Evolution and Conservation of Biodiversity (INCT-EECBio), Goiânia, Goiás, Brazil
| | | | - Sidney F Gouveia
- National Institute of Science and Technology Ecology, Evolution and Conservation of Biodiversity (INCT-EECBio), Goiânia, Goiás, Brazil
- Department of Ecology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
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2
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Tonos J, Papinot B, Park DS, Raelison M, Ramaroson H, Stubbs J, Razafindratsima OH. Examining the structure of plant-lemur interactions in the face of imperfect knowledge. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024:e14323. [PMID: 39045776 DOI: 10.1111/cobi.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 07/25/2024]
Abstract
Biotic interactions, such as plant-animal seed dispersal mutualisms, are essential for ecosystem function. Such interactions are threatened by the possible extinction of the animal partners. Using a data set that includes plant-lemur interactions across Madagascar, we studied the current state of knowledge of these interactions and their structure to determine which plant species are most at risk of losing dispersal services due to the loss of lemurs. We found substantial gaps in understanding of plant-lemur interactions; data were substantially skewed toward a few lemur species and locations. There was also a large gap in knowledge on the interactions of plants and small-bodied or nocturnal lemurs and lemurs outside a few highly studied locations. Of the recorded interactions, a significant portion occurred between lemurs and endemic plants, rather than native or introduced plants. We also found that lemur species tended to primarily consume closely related plant species. Such interaction patterns may indicate the threats to Malagasy endemic plants and highlight how lemur population loss or reductions could affect plant phylogenetic diversity. When examining the impacts of lemur extinction, losing critically endangered species left 164 plant species with no known lemur frugivore partners. Despite phylogenetic patterns in lemur diet, plants for which the only known lemur frugivore is critically endangered were not closely related. These results emphasize the need for further studies to complete our knowledge on these essential interactions and to inform conservation priorities.
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Affiliation(s)
- Jadelys Tonos
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Bastien Papinot
- Tundra Ecology Lab, Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Daniel S Park
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | | | - Herilantonirina Ramaroson
- Zootechnic, Veterinary and Fish Research Department (DRZVP), National Research Institute Applied for Rural Development (FOFIFA / CENRADERU), Antananarivo, Madagascar
| | - Jessica Stubbs
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Onja H Razafindratsima
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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Xu L, Li X, Tang X, Kou Y, Li C, Li J, Yao M, Zhang B, Wang L, Xu H, You C, Li H, Liu S, Zhang L, Liu Y, Huang X, Tu L, Tan B, Xu Z. Consistent community assembly but contingent species pool effects drive β-diversity patterns of multiple microbial groups in desert biocrust systems. Mol Ecol 2024; 33:e17386. [PMID: 38751195 DOI: 10.1111/mec.17386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/21/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
One of the key goals of ecology is to understand how communities are assembled. The species co-existence theory suggests that community β-diversity is influenced by species pool and community assembly processes, such as environmental filtering, dispersal events, ecological drift and biotic interactions. However, it remains unclear whether there are similar β-diversity patterns among different soil microbial groups and whether all these mechanisms play significant roles in mediating β-diversity patterns. By conducting a broad survey across Chinese deserts, we aimed to address these questions by investing biological soil crusts (biocrusts). Through amplicon-sequencing, we acquired β-diversity data for multiple microbial groups, that is, soil total bacteria, diazotrophs, phoD-harbouring taxa, and fungi. Our results have shown varying distance decay rates of β-diversity across microbial groups, with soil total bacteria showing a weaker distance-decay relationship than other groups. The impact of the species pool on community β-diversity varied across microbial groups, with soil total bacteria and diazotrophs being significantly influenced. While the contributions of specific assembly processes to community β-diversity patterns varied among different microbial groups, significant effects of local community assembly processes on β-diversity patterns were consistently observed across all groups. Homogenous selection and dispersal limitation emerged as crucial processes for all groups. Precipitation and soil C:P were the key factors mediating β-diversity for all groups. This study has substantially advanced our understanding of how the communities of multiple microbial groups are structured in desert biocrust systems.
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Affiliation(s)
- Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiangzhen Li
- Engineering Research Centre of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Tang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Chaonan Li
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Jiabao Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Minjie Yao
- Engineering Research Centre of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bingchang Zhang
- Shanxi Normal University, School of Geographical Sciences, Taiyuan, China
| | - Lixia Wang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongwei Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chengming You
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Han Li
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sining Liu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Li Zhang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yang Liu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiong Huang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lihua Tu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Tan
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhenfeng Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Darío Hernandes Córdoba O, Torres-Romero EJ, Villalobos F, Chapa-Vargas L, Santiago-Alarcon D. Energy input, habitat heterogeneity and host specificity drive avian haemosporidian diversity at continental scales. Proc Biol Sci 2024; 291:20232705. [PMID: 38444334 PMCID: PMC10915542 DOI: 10.1098/rspb.2023.2705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
The correct identification of variables affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to test how the taxonomic and phylogenetic diversity and phylogenetic structure of the genera Plasmodium, Haemoproteus and Leucocytozoon from three zoogeographic regions are related to surrogate variables of Earth's energy input, habitat heterogeneity (climatic diversity, landscape heterogeneity, host richness and human disturbance) and ecological interactions (resource use), which was measured by a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that different components of energy input explained variation in richness for each genus. We found that human disturbance influences the phylogenetic structure of Haemoproteus while the degree of generalism explained richness and phylogenetic structure of Plasmodium and Leucocytozoon genera. Furthermore, landscape attributes related to human disturbance (human footprint) can filter Haemoproteus assemblages by their phylogenetic relatedness. Finally, assembly processes related to resource use within parasite assemblages modify species richness and phylogenetic structure of Plasmodium and Leucocytozoon assemblages. Overall, our study highlighted the genus-specific patterns with the different components of Earth's energy budget, human disturbances and degree of generalism.
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Affiliation(s)
| | - Erik Joaquín Torres-Romero
- Laboratorio de Ecología y Conservación de Fauna Silvestre, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, DF, Mexico
- División de Biología, Tecnológico Nacional de México Campus Zacapoaxtla, Subdirección de Investigación y Posgrado, Puebla, Mexico
| | - Fabricio Villalobos
- Red de Biología Evolutiva, Instituto de Ecología, AC Xalapa, Veracruz, Mexico
| | - Leonardo Chapa-Vargas
- División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, AC, San Luis Potosí, Mexico
| | - Diego Santiago-Alarcon
- Department of Integrative Biology, University of South Florida, 12037 USF Beard Drive, SCA 110, Tampa, FL, USA
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Sanjeewani N, Samarasinghe D, Jayasinghe H, Ukuwela K, Wijetunga A, Wahala S, De Costa J. Variation of floristic diversity, community composition, endemism, and conservation status of tree species in tropical rainforests of Sri Lanka across a wide altitudinal gradient. Sci Rep 2024; 14:2090. [PMID: 38267529 PMCID: PMC10808289 DOI: 10.1038/s41598-024-52594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/20/2024] [Indexed: 01/26/2024] Open
Abstract
Tropical rainforests in Sri Lanka are biodiversity hotspots, which are sensitive to anthropogenic disturbance and long-term climate change. We assessed the diversity, endemism and conservation status of these rainforests across a wide altitudinal range (100-2200 m above sea level) via a complete census of all trees having ≥ 10 cm diameter at breast height in ten one-hectare permanent sampling plots. The numbers of tree families, genera and species and community-scale tree diversity decreased with increasing altitude. Tree diversity, species richness and total basal area per ha across the altitudinal range were positively associated with long-term means of maximum temperature, annual rainfall and solar irradiance. Percentage of endangered species increased with increasing altitude and was positively associated with cumulative maximum soil water deficit, day-night temperature difference and high anthropogenic disturbance. Percentage of endemic species was greater in the lowland rainforests than in high-altitude montane forests. Nearly 85% of the species were recorded in three or less plots, which indicated substantial altitudinal differentiation in their distributions. Less than 10 individuals were recorded in 41% of the endemic species and 45% of the native species, which underlined the need for urgent conservation efforts across the whole altitudinal range.
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Affiliation(s)
- Nimalka Sanjeewani
- Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Dilum Samarasinghe
- Postgraduate Institute of Archaeology, University of Kelaniya, Colombo, Sri Lanka
| | | | - Kanishka Ukuwela
- Department of Biological Science, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Asanga Wijetunga
- Department of Biological Science, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Sampath Wahala
- Department of Tourism Management, Faculty of Management Studies, Sabaragamuwa University of Sri Lanka, Belihul Oya, Sri Lanka
| | - Janendra De Costa
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
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Liu XY, Liu SL, Wei HW, Wang XW, Yu J, Shen S, Zhou LW. Preliminary species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi in the Dabie Mountains, Central China reveal unexpected richness. IMA Fungus 2023; 14:23. [PMID: 37964331 PMCID: PMC10644440 DOI: 10.1186/s43008-023-00130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/05/2023] [Indexed: 11/16/2023] Open
Abstract
Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.
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Affiliation(s)
- Xiang-Yang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Hao-Wen Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jia Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China
| | - Shan Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
- College of Life Science, Liaoning University, Shenyang, 110036, People's Republic of China.
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Banerjee AK, Tan F, Feng H, Liang X, Wang J, Yin M, Peng H, Lin Y, Zhang N, Huang Y. Invasive alien plants are phylogenetically distinct from other alien species across spatial and taxonomic scales in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1075344. [PMID: 37745989 PMCID: PMC10513447 DOI: 10.3389/fpls.2023.1075344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
Introduction Phylogenetic relatedness is one of the important factors in the community assembly process. Here, we aimed to understand the large-scale phylogenetic relationship between alien plant species at different stages of the invasion process and how these relationships change in response to the environmental filtering process at multiple spatial scales and different phylogenetic extents. Methods We identified the alien species in three invasion stages, namely invasive, naturalized, and introduced, in China. The occurrence records of the species were used to quantify two abundance-based phylogenetic metrics [the net relatedness index (NRI) and the nearest taxon index (NTI)] from a highly resolved phylogenetic tree. The metrics were compared between the three categories of alien species. Generalized linear models were used to test the effect of climate on the phylogenetic pattern. All analyses were conducted at four spatial scales and for three major angiosperm families. Results We observed significantly higher NRI and NTI values at finer spatial scales, indicating the formation of more clustered assemblages of phylogenetically closely related species in response to the environmental filtering process. Positive NTI values for the invasive and naturalized aliens suggested that the presence of a close relative in the community may help the successful naturalization and invasion of the introduced alien species. In the two-dimensional phylogenetic space, the invasive species communities significantly differed from the naturalized and introduced species, indicating that established alien species need to be phylogenetically different to become invasive. Positive phylogenetic measures for the invasive aliens across the spatial scales suggested that the presence of invasive aliens could facilitate the establishment of other invasive species. Phylogenetic relatedness was more influenced by temperature than precipitation, especially at a finer spatial scale. With decreased temperature, the invasive species showed a more clustered assemblage, indicating conservatism of their phylogenetic niche. The phylogenetic pattern was different at the family level, although there was a consistent tendency across families to form more clustered assemblages. Discussion Overall, our study showed that the community assemblage became more clustered with the progression of the invasion process. The phylogenetic measures varied at spatial and taxonomic scales, thereby highlighting the importance of assessing phylogenetic patterns at different gradients of the community assembly process.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hui Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinru Liang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiakai Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Minghui Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hao Peng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Nannan Zhang
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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Jiang X, Guo X, Lu H, Yang J, Li W, Hao Q. Distinct Community Assembly Mechanisms of Different Growth Stages in a Warm Temperate Forest. DIVERSITY 2023. [DOI: 10.3390/d15040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Community phylogenetic structure and diversity analysis are useful complements to species-centric approaches in biodiversity studies by providing new insights into the processes that drive community assembly. In this study, we aimed to understand the differences in the relative importance of abiotic filtering, biotic interactions, and dispersal limitation on community assembly of trees at different vegetation growth stages. We also examined the influence of geographical distance, elevation, terrain, and soil. Thus, we examined the phylogenetic structures and β-diversities of saplings and adults along different abiotic gradients. The results of the net relatedness index (NRI) showed that, instead of being random, the phylogenetic structure of saplings tended to be convergent, whereas that of adults tended to be divergent. This result implies that the relative forces of abiotic filtering and biotic interactions change throughout vegetation growth. The results of generalized dissimilarity modelling (GDM) showed that dispersal limitation (geographical distance) and abiotic filtering influenced the community assembly of both adults and saplings. This result confirmed our hypothesis that both deterministic and stochastic processes were prevalent. The explanatory rates of geographic distance and environmental factor distance to phylogenetic β-diversity were quite different between adults and saplings, which meant that the relative force of dispersal limitation and abiotic filtering had also changed.
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Affiliation(s)
- Xiaolei Jiang
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiao Guo
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Huicui Lu
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Jinming Yang
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Wei Li
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Qing Hao
- School of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
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Thorley J, Srivastava SK, Shapcott A. What type of rainforest burnt in the South East Queensland's 2019/20 bushfires and how might this impact biodiversity. AUSTRAL ECOL 2023. [DOI: 10.1111/aec.13293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Affiliation(s)
- James Thorley
- GeneCology Research Centre and School of Science, Technology and Engineering University of the Sunshine Coast Maroochydore Queensland Australia
| | - Sanjeev Kumar Srivastava
- GeneCology Research Centre and School of Science, Technology and Engineering University of the Sunshine Coast Maroochydore Queensland Australia
| | - Alison Shapcott
- GeneCology Research Centre and School of Science, Technology and Engineering University of the Sunshine Coast Maroochydore Queensland Australia
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10
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Assessment of the Diversity, Distinctiveness and Conservation of Australia’s Central Queensland Coastal Rainforests Using DNA Barcoding. DIVERSITY 2023. [DOI: 10.3390/d15030378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Globally threatened dry rainforests are poorly studied and conserved when compared to mesic rainforests. Investigations of dry rainforest communities within Australia are no exception. We assessed the community diversity, distinctiveness and level of conservation in Central Queensland coastal dry rainforest communities. Our three-marker DNA barcode-based phylogeny, based on rainforest species from the Central Queensland Coast, was combined with the phylogeny from Southeast Queensland. The phylogenetic tree and Central Queensland Coast (CQC) community species lists were used to evaluate phylogenetic diversity (PD) estimates and species composition to pinpoint regions of significant rainforest biodiversity. We evaluated the patterns and relationships between rainforest communities of the biogeographical areas of Central Queensland Coast and Southeast Queensland, and within and between Subregions. Subsequently, we identified areas of the highest distinctiveness and diversity in phylogenetically even rainforest communities, consistent with refugia, and areas significantly more related than random, consistent with expansion into disturbed or harsher areas. We found clear patterns of phylogenetic clustering that suggest that selection pressures for moisture and geology were strong drivers of rainforest distribution and species diversity. These results showed that smaller dry rainforests in Central Queensland Coast (CQC) represented areas of regional plant migration but were inadequately protected. To sustain species diversity and distribution under intense selection pressures of moisture availability and substrate type throughout this dry and geologically complex region, the future conservation of smaller patches is essential.
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Lin HY, Sun M, Hao YJ, Li D, Gitzendanner MA, Fu CX, Soltis DE, Soltis PS, Zhao YP. Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time. PLANT DIVERSITY 2023; 45:27-35. [PMID: 36876316 PMCID: PMC9975473 DOI: 10.1016/j.pld.2022.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 06/18/2023]
Abstract
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.
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Affiliation(s)
- Han-Yang Lin
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- School of Advanced Study, Taizhou University, Taizhou 318000, China
| | - Miao Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ya-Jun Hao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Daijiang Li
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Matthew A. Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Cheng-Xin Fu
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Yun-Peng Zhao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Wang J, Xu B, Zhang C, Ji Y, Xue Y, Ren Y, Chen Y. Effect of sampling design on estimation of phylogenetic diversity metrics of fish community. Oecologia 2023; 201:129-141. [PMID: 36454330 DOI: 10.1007/s00442-022-05291-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 11/12/2022] [Indexed: 12/03/2022]
Abstract
Phylogenetic diversity has been widely used to explore diversity patterns and assess processes governing the species composition in community. The estimates of many metrics depend on high-quality data collected from well-designed sampling surveys. However, knowledge of impacts of sampling design on estimation of phylogenetic diversity metrics remains unclear. This study is aim to evaluate the influence of sampling design on phylogenetic diversity metrics estimation of fish community. Simple random sampling (SRS), systematic sampling (SS) and stratified random sampling (StRS) with different sampling intensities were chosen and mean pairwise distances (MPD), mean nearest taxon distance (MNTD), phylogenetic diversity (PD), phylogenetic species variability (PSV), phylogenetic species evenness (PSE) and phylogenetic species richness (PSR) were selected. SRS and StRS showed similar impact on phylogenetic diversity indices estimation and performed relatively well for collecting data to estimate phylogenetic diversity. The accuracy and precision of the estimation increased with sampling intensity under SRS and StRS except SS. MNTD was the only metric not underestimated in four seasons. Metrics strongly influenced by species richness were underestimated when sampling intensity was insufficient. MPD, PSV and PSE showed an obvious seasonal change, which was due to the seasonal differences in fish species composition. In cases where under-sampling is suspected or logistically unavoidable, phylogenetic diversity metrics that are relatively insensitive to sampling design (e.g., MPD and PSV) should be prioritized, especially for exploring the temporal variation in fish community. This study reveals it is indispensable to evaluate sampling design when estimating phylogenetic diversity metrics, especially those indices susceptible to species richness.
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Affiliation(s)
- Jiao Wang
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Binduo Xu
- College of Fisheries, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China.
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China.
| | - Chongliang Zhang
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yupeng Ji
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Ying Xue
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yiping Ren
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yong Chen
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
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Beck JJ, Li D, Johnson SE, Rogers D, Cameron KM, Sytsma KJ, Givnish TJ, Waller DM. Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable. AMERICAN JOURNAL OF BOTANY 2022; 109:1991-2005. [PMID: 36254552 PMCID: PMC10099973 DOI: 10.1002/ajb2.16085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 05/08/2023]
Abstract
PREMISE Numerous processes influence plant distributions and co-occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs. METHODS We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed-effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co-occurrence within microsites. RESULTS Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species-environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. CONCLUSIONS Trait-mediated ecological sorting appears to drive temperate-forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait-based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co-occurrences. Strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear to weaken deterministic, niche-based assembly processes at local scales.
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Affiliation(s)
- Jared J. Beck
- Negaunee Institute for Plant Conservation ScienceChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Daijiang Li
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana70808USA
- Center for Computation & TechnologyLouisiana State UniversityBaton RougeLouisiana70808USA
| | | | - David Rogers
- Department of Biological SciencesUniversity of Wisconsin‐ParksideKenoshaWisconsin53144USA
| | - Kenneth M. Cameron
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Kenneth J. Sytsma
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Thomas J. Givnish
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Donald M. Waller
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
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14
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Stochastic Processes Drive Plant Community Assembly in Alpine Grassland during the Restoration Period. DIVERSITY 2022. [DOI: 10.3390/d14100832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Enclosure (prohibition of grazing) is an important process to restore alpine grassland on the Qinghai-Tibetan Plateau. However, few studies have quantified the extent to which the long-term enclosure may contribute to the changes in plant phylogenetic diversity and community assembly in alpine grassland under environmental change. In this study, based on an 11-year fencing experiment along an altitudinal gradient ranging from 4400 m to 5200 m in central Tibet, we conducted an observation of species composition and coverage within and outside the fences in the fifth, eighth and eleventh year, and monitored the related climate and soil factors at 7 sites. Our aim is to quantify the relative effects of environmental change and grassland management on the alpine plant community assemblage. The results were: (1) the overall phylogenetic structure (NRI) of the alpine plant communities, whether inside or outside the enclosure, was divergent at altitudes where the environment was relatively unextreme (4800–5100 m), but aggregative at altitudes with low precipitation (4400–4650 m) or with low temperature (5200 m). (2) The phylogenetic structure of the nearest taxon of species (NTI) was more aggregative along the whole gradient. (3) Precipitation was the dominant factor driving the changes in species richness, phylogenetic diversity and community α-phylogenetic structure indices (NRI and NTI), followed by enclosure duration and soil C:N ratio. (4) The phylogenetic structure of the communities was similar at higher altitudes under grazing or enclosure treatments, and was opposite at lower sites. Stochastic processes have driven the changes in the communities between inside and outside the fences at all altitudes. In addition, homogeneous dispersal occurred in communities at higher sites. In summary, the 11-year enclosure had little effect on community structure of alpine meadows where the grazing pressure is relative lower, whereas it could help restore the community of steppe meadow at lower altitudes where the grazing pressure is extensively higher. This study may provide a vital theoretical support for the formulation of differential management for alpine grassland on the Tibetan Plateau.
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15
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Phylogenetic and Functional Structure of Wood Communities among Different Disturbance Regimes in a Temperate Mountain Forest. FORESTS 2022. [DOI: 10.3390/f13060896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanisms responsible for biodiversity formation and maintenance are central themes in biodiversity conservation. However, the relationships between community assembly, phylogeny, and functional traits remain poorly understood, especially following disturbance. In this study, we examined forest community assembly mechanisms in different disturbance regimes across spatial scales and including tree life history classes, using phylogenetic and functional trait metrics. Across disturbance regimes, phylogenetic structure tended to be over-dispersed, while functional structure tended to be clustered. The over-dispersion of phylogenetic structure also increased from small to large diameter species. Moreover, the explanation of spatial distance for the turnover of phylogenetic and functional structure was increased, while environmental distance explained less structure as disturbance intensity decreased. Our findings suggest that niche theory largely explains forest community assembly in different disturbance regimes. Furthermore, environmental filtering plays a major role in moderate to high disturbance regimes, while competitive exclusion is more important in undisturbed and slightly disturbed ecosystems.
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16
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Mota NM, Gastauer M, Carrión JF, Meira-Neto JAA. Roads as conduits of functional and phylogenetic degradation in Caatinga. Trop Ecol 2022. [DOI: 10.1007/s42965-022-00245-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Si X, Cadotte MW, Davies TJ, Antonelli A, Ding P, Svenning JC, Faurby S. Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late-Quaternary mammal assemblages on oceanic islands. Ecol Lett 2022; 25:1250-1262. [PMID: 35275608 DOI: 10.1111/ele.13997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/29/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco-evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late-Quaternary mammal species. We find island mammal assemblages tend to be phylogenetically clustered (share more recent evolutionary histories), with clustering increasing with island area and isolation. We also observe that mammal assemblages often tend to be functionally clustered (share similar traits), but the strength of clustering is weak and generally independent from island area or isolation. These findings indicate the important roles of in situ speciation and dispersal filtering in shaping island mammal assemblages under pre-anthropogenic conditions, notably through adaptive radiation of a few clades (e.g. bats, with generally high dispersal abilities). Our study demonstrates that considering the functional and phylogenetic axes of diversity can better reveal the eco-evolutionary processes of island community assembly.
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Affiliation(s)
- Xingfeng Si
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming (IEC), Shanghai, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Antonelli
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.,Royal Botanic Gardens, Richmond, Surrey, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Søren Faurby
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
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18
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Shivaprakash KN, Rajanna JM, Gunaga SV, Ravikanth G, Vasudeva R, Shaanker RU, Dayanandan S. The flooded habitat adaptation, niche differentiation, and evolution of Myristicaceae trees in the Western Ghats biodiversity hotspot in India. Biotropica 2022. [DOI: 10.1111/btp.13078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- K. Nagaraju Shivaprakash
- Department of Biology and Centre for Structural & Functional Genomics Concordia University Montreal Quebec Canada
- Quebec Centre for Biodiversity Science Montreal Quebec Canada
- The Nature Conservancy Center New Delhi India
| | - Jagadish M. Rajanna
- Department of Forest Biology College of Forestry University of Agricultural Sciences Sirsi Karnataka India
| | - Srikanth V. Gunaga
- Department of Forest Biology College of Forestry University of Agricultural Sciences Sirsi Karnataka India
| | - Gudasalamani Ravikanth
- Suri Sehgal Centre for Biodiversity and Conservation Ashoka Trust for Research in Ecology and the Environment Bangalore Karnataka India
| | - Ramesh Vasudeva
- Department of Forest Biology College of Forestry University of Agricultural Sciences Sirsi Karnataka India
| | - Ramanan Uma Shaanker
- Department of Crop Physiology and School of Ecology and Conservation University of Agricultural Sciences GKVK Bangalore Karnataka India
| | - Selvadurai Dayanandan
- Department of Biology and Centre for Structural & Functional Genomics Concordia University Montreal Quebec Canada
- Quebec Centre for Biodiversity Science Montreal Quebec Canada
- The Nature Conservancy Center New Delhi India
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19
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Puga-Caballero A, Lara C, Sánchez-González LA. From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00544-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Dambros C, Cáceres N, Baselga A. The prevalence of temperature and dispersal limitation as drivers of diversity in Neotropical small mammals. AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristian Dambros
- Department of Ecology and Evolution CCNE Universidade Federal de Santa Maria 97.105‐900 Santa Maria Brazil
| | - Nilton Cáceres
- Department of Ecology and Evolution CCNE Universidade Federal de Santa Maria 97.105‐900 Santa Maria Brazil
| | - Andrés Baselga
- Departamento de Zoología, Genética y Antropología Física Universidad de Santiago de Compostela Santiago de Compostela Spain
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21
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Simpson EG, Pearse WD. Fractal triads efficiently sample ecological diversity and processes across spatial scales. OIKOS 2021. [DOI: 10.1111/oik.08272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - William D. Pearse
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Life Sciences, Imperial College London, Silwood Park Campus Ascot Berkshire UK
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22
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Lehtonen S, Muscarella R, Moulatlet G, Balslev H, Tuomisto H. Edaphic heterogeneity and the evolutionary trajectory of Amazonian plant communities. Ecol Evol 2021; 11:17672-17685. [PMID: 35003631 PMCID: PMC8717337 DOI: 10.1002/ece3.8477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
We investigated how the phylogenetic structure of Amazonian plant communities varies along an edaphic gradient within the non-inundated forests. Forty localities were sampled on three terrain types representing two kinds of soil: clayey soils of a high base cation concentration derived from the Solimões formation, and loamy soils with lower base cation concentration derived from the Içá formation and alluvial terraces. Phylogenetic community metrics were calculated for each locality for ferns and palms both with ferns as one group and for each of three fern clades with a crown group age comparable to that of palms. Palm and fern communities showed significant and contrasting phylogenetic signals along the soil gradient. Fern species richness increased but standard effect size of mean pairwise distance (SES.MPD) and variation of pairwise distances (VPD) decreased with increasing soil base cation concentration. In contrast, palm communities were more species rich on less cation-rich soils and their SES.MPD increased with soil base cation concentration. Species turnover between the communities reflected the soil gradient slightly better when based on species occurrences than when phylogenetic distances between the species were considered. Each of the three fern subclades behaved differently from each other and from the entire fern clade. The fern clade whose phylogenetic patterns were most similar to those of palms also resembled palms in being most species-rich on cation-poor soils. The phylogenetic structuring of local plant communities varies along a soil base cation concentration gradient within non-inundated Amazonian rain forests. Lineages can show either similar or different phylogenetic community structure patterns and evolutionary trajectories, and we suggest this to be linked to their environmental adaptations. Consequently, geological heterogeneity can be expected to translate into a potentially highly diverse set of evolutionarily distinct community assembly pathways in Amazonia and elsewhere.
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Affiliation(s)
| | - Robert Muscarella
- Plant Ecology and EvolutionEvolutionary Biology CenterUppsala UniversityUppsalaSweden
| | - Gabriel Moulatlet
- Facultad de Ciencias de la Tierra y AguaUniversidad Regional Amazónica IkiamTenaEcuador
| | - Henrik Balslev
- Section for Ecoinformatics & BiodiversityDepartment of BioscienceAarhus UniversityAarhusDenmark
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23
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Pfenning-Butterworth AC, Davies TJ, Cressler CE. Identifying co-phylogenetic hotspots for zoonotic disease. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200363. [PMID: 34538148 PMCID: PMC8450626 DOI: 10.1098/rstb.2020.0363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host-parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host-parasite association data with host and parasite phylogenies. Here, we use host-parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host-parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
| | - T. Jonathan Davies
- Departments of Botany, Forest, and Conservation Science, University of British Columbia, Vancouver, British Columbia, Canada
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24
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Pontarp M. Ecological opportunity and adaptive radiations reveal eco-evolutionary perspectives on community structure in competitive communities. Sci Rep 2021; 11:19560. [PMID: 34599238 PMCID: PMC8486866 DOI: 10.1038/s41598-021-98842-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022] Open
Abstract
It is well known that ecological and evolutionary processes act in concert while shaping biological communities. Diversification can, for example, arise through ecological opportunity and adaptive radiations and competition play an essential role in such diversification. Eco-evolutionary components of competition are thus important for our understanding of community assembly. Such understanding in turn facilitates interpretation of trait- and phylogenetic community patterns in the light of the processes that shape them. Here, I investigate the link between competition, diversification, and trait- and phylogenetic- community patterns using a trait-based model of adaptive radiations. I evaluate the paradigm that competition is an ecological process that drives large trait- and phylogenetic community distances through limiting similarity. Contrary to the common view, I identify low or in some cases counterintuitive relationships between competition and mean phylogenetic distances due to diversification late in evolutionary time and peripheral parts of niche space when competition is weak. Community patterns as a function of competition also change as diversification progresses as the relationship between competition and trait similarity among species can flip from positive to negative with time. The results thus provide novel perspectives on community assembly and emphasize the importance of acknowledging eco-evolutionary processes when interpreting community data.
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Affiliation(s)
- Mikael Pontarp
- Department of Biology, Lund University Biology Building, Sölvegatan 35, 223 62, Lund, Sweden.
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25
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Cao JH, Qi R, Liu T, Li B, Gao BQ, Chen XL, Zhao Y, Zhao ZG. Patterns of species and phylogenetic diversity in Picea purpurea forests under different levels of disturbance on the northeastern Qinghai-Tibetan Plateau. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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26
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Ma Y, Wang M, Wei F, Nie Y. Geographic distributions shape the functional traits in a large mammalian family. Ecol Evol 2021; 11:13175-13185. [PMID: 34646461 PMCID: PMC8495830 DOI: 10.1002/ece3.8039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/27/2023] Open
Abstract
Traits of organisms are shaped by their living environments and also determined in part by their phylogenetic relationships. For example, phylogenetic relationships often affect the geographic distributions of animals and cause variation in their living environments, which usually play key roles in the life history and determine the functional traits of species. As an ancient family of mammals, bears widely distribute and have evolved some specific strategies for survival and reproduction during their long-term evolutionary histories. Many studies on the ecology of bears have been conducted in recent decades, but few have focused on the relationships between their geographic distributions and ecological adaptations. Here, using bears as a model system, we collected and reanalyzed data from the available literatures to explore how geographic distributions and phylogenetic relationships shape the functional traits of animals. We found a positive relationship between phylogenetic relatedness and geographic distributions, with bears distributed in adjacent areas applying more similar strategies to survive and reproduce: (a) Bears living at high latitudes consumed a higher proportion of vertebrates, which may provide more fat for adaptation to low temperatures, and (b) their reproduction rhythms follow fluctuations in seasonal forage availability and quality, in which bears reach mating status from March to May and give birth in approximately November or later.
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Affiliation(s)
- Yingjie Ma
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Meng Wang
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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27
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Adamo I, Castaño C, Bonet JA, Colinas C, Martínez de Aragón J, Alday JG. Lack of Phylogenetic Differences in Ectomycorrhizal Fungi among Distinct Mediterranean Pine Forest Habitats. J Fungi (Basel) 2021; 7:jof7100793. [PMID: 34682215 PMCID: PMC8538088 DOI: 10.3390/jof7100793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding whether the occurrences of ectomycorrhizal species in a given tree host are phylogenetically determined can help in assessing different conservational needs for each fungal species. In this study, we characterized ectomycorrhizal phylogenetic composition and phylogenetic structure in 42 plots with five different Mediterranean pine forests: i.e., pure forests dominated by P. nigra, P. halepensis, and P. sylvestris, and mixed forests of P. nigra-P. halepensis and P. nigra-P. sylvestris, and tested whether the phylogenetic structure of ectomycorrhizal communities differs among these. We found that ectomycorrhizal communities were not different among pine tree hosts neither in phylogenetic composition nor in structure and phylogenetic diversity. Moreover, we detected a weak abiotic filtering effect (4%), with pH being the only significant variable influencing the phylogenetic ectomycorrhizal community, while the phylogenetic structure was slightly influenced by the shared effect of stand structure, soil, and geographic distance. However, the phylogenetic community similarity increased at lower pH values, supporting that fewer, closely related species were found at lower pH values. Also, no phylogenetic signal was detected among exploration types, although short and contact were the most abundant types in these forest ecosystems. Our results demonstrate that pH but not tree host, acts as a strong abiotic filter on ectomycorrhizal phylogenetic communities in Mediterranean pine forests at a local scale. Finally, our study shed light on dominant ectomycorrhizal foraging strategies in drought-prone ecosystems such as Mediterranean forests.
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Affiliation(s)
- Irene Adamo
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Correspondence:
| | - Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden;
| | - José Antonio Bonet
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
| | - Carlos Colinas
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Juan Martínez de Aragón
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Josu G. Alday
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
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28
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Qian H, Jin Y. Are phylogenies resolved at the genus level appropriate for studies on phylogenetic structure of species assemblages? PLANT DIVERSITY 2021; 43:255-263. [PMID: 34485767 PMCID: PMC8390917 DOI: 10.1016/j.pld.2020.11.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 05/06/2023]
Abstract
Phylogenies are essential to studies investigating the effect of evolutionary history on assembly of species in ecological communities and geographical and ecological patterns of phylogenetic structure of species assemblages. Because phylogenies well resolved at the species level are lacking for many major groups of organisms such as vascular plants, researchers often generate a species-level phylogenies using a phylogeny well resolved at the genus level as a backbone and attaching species to their respective genera in the phylogeny as polytomies or by using a megaphylogeny well resolved at the genus level as a backbone and adding additional species to the megaphylogeny as polytomies of their respective genera. However, whether the result of a study using species-level phylogenies generated in these ways is robust, compared to that based on phylogenies fully resolved at the species level, has not been assessed. Here, we use 1093 angiosperm tree assemblages (each in a 110 × 110 km quadrat) in North America as a model system to address this question, by examining six commonly used metrics of phylogenetic structure (phylogenetic diversity and phylogenetic relatedness) and six climate variables commonly used in ecology. Our results showed that (1) the scores of phylogenetic metrics derived from species-level phylogenies resolved at the genus level with species being attached to their respective genera as polytomies are very strongly or perfectly correlated to those derived from a phylogeny fully resolved at the species level (the mean of correlation coefficients is 0.973), and (2) the relationships between the scores of phylogenetic metrics and climate variables are consistent between the two sets of analyses based on the two types of phylogeny. Our study suggests that using species-level phylogenies resolved at the genus level with species being attached to their genera as polytomies is appropriate in studies exploring patterns of phylogenetic structure of species in ecological communities across geographical and ecological gradients.
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Affiliation(s)
- Hong Qian
- Research and Collections Center, Illinois State Museum, 1011 East Ash Street, Springfield, IL, 62703, USA
| | - Yi Jin
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550025, China
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29
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Jin L, Liu JJ, Xiao TW, Li QM, Lin LX, Shao XN, Ma CX, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Hao G, Ge XJ. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China. Mol Ecol Resour 2021; 22:319-333. [PMID: 34233085 DOI: 10.1111/1755-0998.13462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
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Affiliation(s)
- Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yu Lian
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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30
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Matthews A, Majeed A, Barraclough TG, Raymond B. Function is a better predictor of plant rhizosphere community membership than 16S phylogeny. Environ Microbiol 2021; 23:6089-6103. [PMID: 34190398 DOI: 10.1111/1462-2920.15652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Rhizobacterial communities are important for plant health but we still have limited understanding of how they are constructed or how they can be manipulated. High-throughput 16S rRNA sequencing provides good information on taxonomic composition but remains an unreliable proxy for phenotypes. In this study, we tested the hypothesis that experimentally observed functional traits would be better predictors of community membership than phylogenetic origin. To test this hypothesis, we sampled communities on four plant species grown in two soil types and characterized 593 bacterial isolates in terms of antibiotic susceptibility, carbon metabolism, resource use and plant growth-promoting traits. In support of our hypothesis we found that three of the four plant species had phylogenetically diverse, but functionally constrained communities. Notably, communities did not grow best on complex media mimicking their host of origin but were distinguished by variation in overall growth characteristics (copiotrophy/oligotrophy) and antibiotic susceptibility. These data, combined with variation in phylogenetic structure, suggest that different classes of traits (antagonistic competition or resource-based) are more important in different communities. This culture-based approach supports and complements the findings of a previous high-throughput 16S rRNA analysis of this experiment and provides functional insights into the patterns observed with culture-independent methods.
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Affiliation(s)
- Andrew Matthews
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Afshan Majeed
- Department of Soil and Environmental Sciences, University of the Poonch, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | | | - Ben Raymond
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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31
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Zepeda V, Martorell C. Effects of Phylogenetic Relatedness on Fluctuation-Dependent and Fluctuation-Independent Coexistence Mechanisms in Multispecies Communities. Am Nat 2021; 198:E1-E11. [PMID: 34143720 DOI: 10.1086/714161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractEvolutionary relatedness may hinder stable coexistence due to similar niches and nonlinear responses to competition. The mechanisms driving stability may respond differently to phylogenetic distance. Related species may be synchronic (have similar demographic responses over time), affecting fluctuation-dependent mechanisms: the storage effect should destabilize coexistence, and relative nonlinearity should be stronger due to increased fluctuations in competition. We tested these hypotheses using invasion analysis based on a model parameterized for 19 plant species from a semiarid grassland. Although weakly, coexistence stability increased with phylogenetic distance. Stabilization through fluctuation-independent niche differentiation was stronger between distant relatives as a result of weaker competition. Synchronicity was higher between close relatives, having the expected negative effects on the storage effect's contribution to coexistence. Relative nonlinearity was strong at both ends of the phylogenetic relatedness gradient but not in the middle. This may be the result of different nonlinear responses between distant relatives and of stronger fluctuations in competition due to synchronicity between closer relatives. The effect of phylogenetic distance on coexistence was almost negligible when pairwise species were analyzed, in accordance with previous research. Phylogenetic distance became more important as more species interacted, however, suggesting that evolutionary relatedness may be influential in species-rich communities.
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32
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Amaral EJ, Franco AC, Rivera VL, Munhoz CBR. Environment, phylogeny, and photosynthetic pathway as determinants of leaf traits in savanna and forest graminoid species in central Brazil. Oecologia 2021; 197:1-11. [PMID: 33885981 DOI: 10.1007/s00442-021-04923-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/13/2021] [Indexed: 12/01/2022]
Abstract
Leaf traits are closely linked to plant responses to the environment and can provide important information on adaptation and evolution. These traits may also result from common ancestry, so phylogenetic relationships also play an important role in adaptive evolution. We evaluated the effects of the closed forest environment (gallery forest) and the open savanna environment (cerrado) on the selection of leaf traits of graminoid species. The two plant communities differ in light, nutrients, and water availability, which are important drivers in the selection and differentiation of these traits. We also investigated the functional structure and the role of phylogeny in the functional organization of species, considering leaf traits. Patterns of leaf trait variation differed between forest and savanna species suggesting habitat specialization. Wider and longer leaves, with higher values of specific leaf area, chlorophyll, and nitrogen, seem to be an advantage for graminoid species growing in forest environments, while thicker leaves, with higher values of leaf dry-matter content and carbon, benefit species growing in savanna environments. We found few phylogenetic signals related to leaf traits in each environment. Therefore, the functional similarity that the gallery forest and cerrado graminoid species share within their group is independent of their phylogenetic proximity. Environmental filters affect the functional structure of communities differently, generating communities with trait values that are more distant than expected by chance in cerrado (functional dispersion), and closer than expected by chance in the gallery forest (functional convergence).
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Affiliation(s)
- Eliel J Amaral
- Graduate Program in Ecology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil.
| | - Augusto C Franco
- Graduate Program in Ecology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil.,Department of Botany, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Vanessa L Rivera
- Department of Botany, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Cássia B R Munhoz
- Graduate Program in Ecology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil.,Department of Botany, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
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33
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Heimpel GE, Abram PK, Brodeur J. A phylogenetic perspective on parasitoid host ranges with implications for biological control. CURRENT OPINION IN INSECT SCIENCE 2021; 44:95-100. [PMID: 33901732 DOI: 10.1016/j.cois.2021.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
Interactions that shape parasitoid host ranges occur within the context of both host and parasitoid phylogenetic history. While host-associated speciation of parasitoids can lead to increased host specificity, it can also lead to a broadening of host range through radiation onto a new group of host species. In both cases, sister-species of parasitoids may have widely divergent host ranges. But how should host range be estimated? Traditional views of host ranges as simple lists of species have given way to analyses that can detect host phylogenetic signal. Host relatedness can also be codified into useful indices that reflect the phylogenetic breadth of host range. All of these considerations have important implications for biological control, particularly in the realm of risk assessment.
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Affiliation(s)
- George E Heimpel
- Dept. of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul MN, 55108, USA.
| | - Paul K Abram
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, 6947 Hwy #7, Agassiz, BC, Canada
| | - Jacques Brodeur
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, QC, Canada
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34
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Nascimento ELDL, Maia LC, Cáceres MEDS, Lücking R. Phylogenetic structure of lichen metacommunities in Amazonian and Northeast Brazil. Ecol Res 2021. [DOI: 10.1111/1440-1703.12206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Leonor Costa Maia
- Center of Biosciences, Department of Mycology Federal University of Pernambuco Recife Pernambuco Brazil
| | | | - Robert Lücking
- Botanic Garden and Botanical Museum Freie Universität Berlin Berlin Germany
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35
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Massante JC, Köbel M, Pinho P, Gerhold P, Branquinho C, Nunes A. Phylogenetic structure of understorey annual and perennial plant species reveals opposing responses to aridity in a Mediterranean biodiversity hotspot. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:144018. [PMID: 33352349 DOI: 10.1016/j.scitotenv.2020.144018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Aridity is a critical driver of the diversity and composition of plant communities. However, how aridity influences the phylogenetic structure of functional groups (i.e. annual and perennial species) is far less understood than its effects on species richness. As perennials have to endure stressful conditions during the summer drought, as opposed to annuals that avoid it, they may be subjected to stronger environmental filtering. In contrast, annuals may be more susceptible to interannual climatic variability. Here we studied the phylogenetic structure of the annual and perennial components of understorey plant communities, along a regional aridity gradient in Mediterranean drylands. Specifically, we asked: (1) How do species richness (S) and phylogenetic structure (PS) of annuals and perennials in plant communities respond to aridity? (2) What is the contribution of other climatic and topo-edaphic variables in predicting S and PS for both components? (3) How does the taxonomic and phylogenetic turnover of annuals and perennials vary with spatial and environmental distances? We assessed annuals' and perennials' species richness, the phylogenetic structure at deep and shallow phylogenetic levels, and taxonomic and phylogenetic turnover along spatial and environmental distances. We found no relationship between annuals' richness and aridity, whereas perennials' richness showed a unimodal pattern. The phylogenetic structure of annuals and perennials showed contrasting responses to aridity and negatively correlated with topo-edaphic variables. We found phylogenetic clustering at intermediate-to-higher aridity levels for annuals, and at lower aridity levels for perennials. Both taxonomic and phylogenetic turnover in annuals and perennials correlated with the environmental distance rather than with spatial distance between communities, suggesting adaptation to local factors. Overall, our results show a decoupling in the response of the phylogenetic structure of annual and perennial components of plant communities to aridity in Mediterranean drylands. Our findings have significant implications for land management strategies under climate change.
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Affiliation(s)
- Jhonny Capichoni Massante
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu 51014, Estonia; Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal.
| | - Melanie Köbel
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal
| | - Pille Gerhold
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu 51014, Estonia; Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal
| | - Alice Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Piso 5, 1749-016 Lisboa, Portugal
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36
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Junggebauer A, Hartke TR, Ramos D, Schaefer I, Buchori D, Hidayat P, Scheu S, Drescher J. Changes in diversity and community assembly of jumping spiders (Araneae: Salticidae) after rainforest conversion to rubber and oil palm plantations. PeerJ 2021; 9:e11012. [PMID: 33717710 PMCID: PMC7937343 DOI: 10.7717/peerj.11012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/05/2021] [Indexed: 11/20/2022] Open
Abstract
Rainforest conversion into monoculture plantations results in species loss and community shifts across animal taxa. The effect of such conversion on the role of ecophysiological properties influencing communities, and conversion effects on phylogenetic diversity and community assembly mechanisms, however, are rarely studied in the same context. Here, we compare salticid spider (Araneae: Salticidae) communities between canopies of lowland rainforest, rubber agroforest (“jungle rubber”) and monoculture plantations of rubber or oil palm, sampled in a replicated plot design in Jambi Province, Sumatra, Indonesia. Overall, we collected 912 salticid spider individuals and sorted them to 70 morphospecies from 21 genera. Salticid richness was highest in jungle rubber, followed by rainforest, oil palm and rubber, but abundance of salticids did not differ between land-use systems. Community composition was similar in jungle rubber and rainforest but different from oil palm and rubber, which in turn were different from each other. The four investigated land-use systems differed in aboveground plant biomass, canopy openness and land use intensity, which explained 12% of the observed variation in canopy salticid communities. Phylogenetic diversity based on ~850 bp 28S rDNA fragments showed similar patterns as richness, that is, highest in jungle rubber, intermediate in rainforest, and lowest in the two monoculture plantations. Additionally, we found evidence for phylogenetic clustering of salticids in oil palm, suggesting that habitat filtering is an important factor shaping salticid spider communities in monoculture plantations. Overall, our study offers a comprehensive insight into the mechanisms shaping communities of arthropod top predators in canopies of tropical forest ecosystems and plantations, combining community ecology, environmental variables and phylogenetics across a land-use gradient in tropical Asia.
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Affiliation(s)
- André Junggebauer
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Tamara R Hartke
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Daniel Ramos
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Ina Schaefer
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Damayanti Buchori
- Department of Plant Protection, Faculty of Agriculture, Bogor Agricultural University, Bogor, Indonesia.,Center for Transdisciplinary and Sustainability Sciences, IPB University, Bogor, Indonesia
| | - Purnama Hidayat
- Department of Plant Protection, Faculty of Agriculture, Bogor Agricultural University, Bogor, Indonesia
| | - Stefan Scheu
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
| | - Jochen Drescher
- Department of Animal Ecology, J-F. Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen, Germany
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37
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Davies TJ. Ecophylogenetics redux. Ecol Lett 2021; 24:1073-1088. [PMID: 33565697 DOI: 10.1111/ele.13682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 12/24/2022]
Abstract
Species' evolutionary histories shape their present-day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances - communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning - with relevance for conservation and restoration - and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive.
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Affiliation(s)
- T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, 2092, South Africa
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Diversity, Co-Occurrence, and Nestedness Patterns of Sand Fly Species (Diptera: Psychodidae) in Two Rural Areas of Western Panamá. INSECTS 2021; 12:insects12020113. [PMID: 33525399 PMCID: PMC7912352 DOI: 10.3390/insects12020113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/30/2022]
Abstract
Simple Summary Sand flies are insects that can transmit the parasites causing leishmaniasis, a major neglected tropical disease. In the Americas, these insects are highly diverse, and unlike what is observed for other vector-borne diseases, many species co-occur in sites where this disease affects human populations. Here, we present results from a two-year-long study where we study how the number of species changes in two rural areas of Western Panamá with different land use cover and through the dry and wet seasons. We found that species number increased during the wet season and in plots with higher natural forest cover and that species number decreased in both areas in plots when the forest cover decreased, with some species changing through the seasons, and some species disappearing when comparing the sand fly faunas of the most forested with less forested plots. However, our results suggest that seasonality, or the change from a dry to rainy season, can be a more important driver of the number of species locally observed in the studied areas. Abstract Cutaneous Leishmaniasis transmission in the New World is observed in areas with rich sand fly species’ faunas. The diversity and composition of sand fly species can change in response to seasonal weather and land use changes. Here, we present results from a two-year-long study where we collected, using Centers for Disease Control (CDC) light traps, sand flies from two rural areas, Las Pavas (LP) and Trinidad de las Minas (T) in western Panamá. Over 710 trap-nights, we collected 16,156 sand flies from 15 genera and 35 species. We identified 34 species in T, and the most abundant species collected was Nyssomyia trapidoi (Fairchild and Hertig, 1952) (n = 2278, 37%), followed by Psychodopygus panamensis (Shannon, 1926) (n = 1112, 18%), and Trichopygomyia triramula (Fairchild and Hertig, 1952) (n = 1063, 17%). In LP, we identified 26 species, and the most abundant species collected were Ty. triramula (n = 4729, 48%), and Ps. panamensis (n = 3444, 35%). We estimated a higher species’ richness in T (Chao2 ± S.E.: 36.58 ± 3.84) than in LP (27.49 ± 2.28). In T, species’ richness was significantly higher in the rainy season, but no seasonal differences were observed in LP. Species’ assemblages were nested in the two areas. Phlebotomine sand fly species’ abundance increased at the two sites during the rainy season. Our data suggest that seasonality is more important than land use as a factor driving sand fly species’ diversity at the studied sites.
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Hatmaker EA, Wadl PA, Rinehart TA, Carroll J, Lane TS, Trigiano RN, Staton ME, Schilling EE. Complete chloroplast genome comparisons for Pityopsis (Asteraceae). PLoS One 2020; 15:e0241391. [PMID: 33370297 PMCID: PMC7769439 DOI: 10.1371/journal.pone.0241391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/13/2020] [Indexed: 12/03/2022] Open
Abstract
Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Phillip A. Wadl
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, United States of America
| | - Timothy A. Rinehart
- U.S. Department of Agriculture, Agricultural Research Service, Crop Production and Protection, Beltsville, Maryland, United States of America
| | - Jennifer Carroll
- U.S. Department of Agriculture, Agricultural Research Service, Thad Cochran Southern Horticultural Laboratory, Poplarville, Mississippi, United States of America
| | - Thomas S. Lane
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
| | - Edward E. Schilling
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail: (RNT); (MES); (EES)
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Adorno BFCB, Barros FM, Cezar Ribeiro M, Silva VX, Hasui É. Landscape heterogeneity shapes bird phylogenetic responses at forest–matrix interfaces in Atlantic Forest, Brazil. Biotropica 2020. [DOI: 10.1111/btp.12881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - Fábio M. Barros
- CPEA (Consultoria, Planejamento e Estudos Ambientais) São Paulo Brazil
| | - Milton Cezar Ribeiro
- Laboratório de Ecologia Espacial e Conservação (LEEC) Departamento de Biodiversidade Instituto de Biociências Universidade Estadual Paulista (UNESP) Rio Claro Brazil
| | - Vinícius X. Silva
- Instituto de Ciências da NaturezaUniversidade Federal de Alfenas Alfenas Brazil
| | - Érica Hasui
- Instituto de Ciências da NaturezaUniversidade Federal de Alfenas Alfenas Brazil
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Vesterinen EJ, Kaunisto KM, Lilley TM. A global class reunion with multiple groups feasting on the declining insect smorgasbord. Sci Rep 2020; 10:16595. [PMID: 33024156 PMCID: PMC7539006 DOI: 10.1038/s41598-020-73609-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/15/2020] [Indexed: 12/05/2022] Open
Abstract
We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.
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Affiliation(s)
- Eero J Vesterinen
- Department of Biology, University of Turku, Turku, Finland.
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Thomas M Lilley
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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Kaplan I, Bokulich NA, Caporaso JG, Enders LS, Ghanem W, Ingerslew KS. Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evol Appl 2020; 13:1984-1999. [PMID: 32908599 PMCID: PMC7463318 DOI: 10.1111/eva.12956] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/17/2022] Open
Abstract
Agriculture has long employed phylogenetic rules whereby farmers are encouraged to rotate taxonomically unrelated plants in shared soil. Although this forms a central tenet of sustainable agriculture, strangely, this on-farm "rule of thumb" has never been rigorously tested in a scientific framework. To experimentally evaluate the relationship between phylogenetic distance and crop performance, we used a plant-soil feedback approach whereby 35 crops and weeds varying in their relatedness to tomato (Solanum lycopersicum) were tested in a two-year field experiment. We used community profiling of the bacteria and fungi to determine the extent to which soil microbes contribute to phenotypic differences in crop growth. Overall, tomato yield was ca. 15% lower in soil previously cultivated with tomato; yet, past the species level there was no effect of phylogenetic distance on crop performance. Soil microbial communities, on the other hand, were compositionally more similar between close plant relatives. Random forest regression predicted log10 phylogenetic distance to tomato with moderate accuracy (R 2 = .52), primarily driven by bacteria in the genus Sphingobium. These data indicate that, beyond avoiding conspecifics, evolutionary history contributes little to understanding plant-soil feedbacks in agricultural fields; however, microbial legacies can be predicted by species identity and relatedness.
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Affiliation(s)
- Ian Kaplan
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
| | - Nicholas A. Bokulich
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | - J. Gregory Caporaso
- Center for Applied Microbiome ScienceThe Pathogen and Microbiome InstituteNorthern Arizona UniversityFlagstaffAZUSA
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | | | - Wadih Ghanem
- Department of EntomologyPurdue UniversityWest LafayetteINUSA
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Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research. DIVERSITY 2020. [DOI: 10.3390/d12080288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.
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Starko S, Demes KW, Neufeld CJ, Martone PT. Convergent evolution of niche structure in Northeast Pacific kelp forests. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Samuel Starko
- Department of Botany & Biodiversity Research Centre University of British Columbia Vancouver BC Canada
- Department of Biology University of Victoria Victoria BC Canada
- Bamfield Marine Sciences Centre Bamfield BC Canada
| | - Kyle W. Demes
- Institutional Strategic Awards Simon Fraser University Burnaby BC Canada
| | | | - Patrick T. Martone
- Department of Botany & Biodiversity Research Centre University of British Columbia Vancouver BC Canada
- Bamfield Marine Sciences Centre Bamfield BC Canada
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Abstract
AbstractHuman-mediated species invasion and climate change are leading to global extinctions and are predicted to result in the loss of important axes of phylogenetic and functional diversity. However, the long-term robustness of modern communities to invasion is unknown, given the limited timescales over which they can be studied. Using the fossil record of the Paleocene-Eocene thermal maximum (PETM; ∼56 Ma) in North America, we evaluate mammalian community-level response to a rapid global warming event (5°-8°C) and invasion by three Eurasian mammalian orders and by species undergoing northward range shifts. We assembled a database of 144 species body sizes and created a time-scaled composite phylogeny. We calculated the phylogenetic and functional diversity of all communities before, during, and after the PETM. Despite increases in the phylogenetic diversity of the regional species pool, phylogenetic diversity of mammalian communities remained relatively unchanged, a pattern that is invariant to the tree dating method, uncertainty in tree topology, and resolution. Similarly, body size dispersion and the degree of spatial taxonomic turnover of communities remained similar across the PETM. We suggest that invasion by new taxa had little impact on Paleocene-Eocene mammal communities because niches were not saturated. Our findings are consistent with the numerous studies of modern communities that record little change in community-scale richness despite turnover in taxonomic composition during invasion. What remains unknown is whether long-term robustness to biotic and abiotic perturbation are retained by modern communities given global anthropogenic landscape modification.
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Jin LS, Yin D, Fortin MJ, Cadotte MW. The mechanisms generating community phylogenetic patterns change with spatial scale. Oecologia 2020; 193:655-664. [PMID: 32621030 DOI: 10.1007/s00442-020-04695-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 06/16/2020] [Indexed: 10/23/2022]
Abstract
Studies that test community assembly hypotheses in observational communities frequently evaluate patterns for plots or entire communities, yet studies that examine assembly patterns across spatial scales show that they are greatly influenced by scale. Here, we test the spatial dependency of patterns of relatedness and plant height for all individual herbaceous plants along five 40-m old-field transects (Southern Ontario, Canada). We identified each individual plant and measured its distance along the transect and its height, and we constructed a molecular phylogeny for all observed species. To uncover the scale at which community phylogenetic and trait similarities shift, we used partial Mantel correlograms and distance-based Moran Eigenvector Maps (dbMEMs). We found that communities shift from significantly overdispersed at relatively smaller scales (i.e., < 15 m) to spatially clustered at larger scales, showing that assembly mechanism influence depends on scale of observation. This pattern was observed for both phylogeny and height, but was the strongest when considering phylogeny only. These results reveal the importance of spatial scale when examining community phylogenetic or trait patterns, where finding support for one assembly mechanism at a single scale does not necessarily mean that other mechanisms are also not important for structuring community composition and diversity.
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Affiliation(s)
- Lanna S Jin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Deyi Yin
- Department of Biological Sciences, University of Toronto at Scarborough, Scarborough, 416-208-5105, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Marc W Cadotte
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada. .,Department of Biological Sciences, University of Toronto at Scarborough, Scarborough, 416-208-5105, Canada.
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Pinto‐Ledezma JN, Villalobos F, Reich PB, Catford JA, Larkin DJ, Cavender‐Bares J. Testing Darwin’s naturalization conundrum based on taxonomic, phylogenetic, and functional dimensions of vascular plants. ECOL MONOGR 2020. [DOI: 10.1002/ecm.1420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jesús N. Pinto‐Ledezma
- Department of Ecology, Evolution and Behavior University of Minnesota 1479 Gortner Avenue Saint Paul Minnesota 55108 USA
| | - Fabricio Villalobos
- Red de Biología Evolutiva Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya 91070Xalapa Veracruz México
| | - Peter B. Reich
- Department of Forest Resources University of Minnesota 1530 Cleveland Avenue Saint Paul Minnesota 55108 USA
- Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales 2753 Australia
| | - Jane A. Catford
- Department of Geography King’s College London Strand London WC2B 4BG UK
| | - Daniel J. Larkin
- Department of Fisheries, Wildlife, and Conservation Biology University of Minnesota 135 Skok Hall, 2003 Upper Buford Circle Saint Paul Minnesota 55108 USA
| | - Jeannine Cavender‐Bares
- Department of Ecology, Evolution and Behavior University of Minnesota 1479 Gortner Avenue Saint Paul Minnesota 55108 USA
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Zhang Q, Holyoak M, Goodale E, Liu Z, Shen Y, Liu J, Zhang M, Dong A, Zou F. Trait-environment relationships differ between mixed-species flocking and nonflocking bird assemblages. Ecology 2020; 101:e03124. [PMID: 32564355 DOI: 10.1002/ecy.3124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/06/2020] [Accepted: 05/05/2020] [Indexed: 12/27/2022]
Abstract
Hypotheses about the mechanisms of community assembly suggest that biotic and abiotic filters constrain species establishment through selection on their functional traits. It is unclear how differences in traits influence the niche dimensions of closely related bird species when they coexist in spatiotemporally heterogeneous environments. Further, it is necessary to take into account their participation in mixed-species flocks, social systems that can include both competition and facilitation. For 6 yr, we conducted counts of forest bird species and took measurements of environmental variables along an elevational gradient in the Nanling Mountains, China. To disentangle different deterministic and historical/stochastic processes between flocking and nonflocking bird assemblages, we first compared phylogenetic and functional structure, and community-weighted mean trait values (CWM). We further assessed elevational variations in trait-environment relationships. We found that the flocking and nonflocking bird assemblages were structured by environmental gradients in contrasting ways. The nonflocking assemblage showed a strong change from over-dispersed to clustered community structure with increasing elevations, consistent with the strong selective pressures of a harsh environment (i.e., environmental filtering). The nonflocking assemblage also displayed significant trait-environment relationships in bivariate correlations and multivariate ordination space, including specific morphological and foraging traits that are linked to vegetation characteristics (e.g., short trees at high elevations). By contrast, flocking birds were more resilient to habitat change with elevation, with relatively consistent community membership, and showed fewer trait-environment associations. CWM of traits that are known to be associated with species' propensity to join mixed-species flocks, including small body size and broad habitat specificity, were linked to the flocking assemblage consistently across the elevational gradient. Collectively, our trait-based analyses provide strong evidence that trait-environment relationships differ between flocking and nonflocking bird assemblages. Besides serving as bellwethers of changing environments, emergent properties of flock systems may increase the resilience of animal communities undergoing environmental change. Mixed-species flocks present an ideal model with which to explore cooccurrence of closely related species, because habitat filtering may be buffered, and the patterns observed are therefore the outcomes of species interactions including both competition and facilitation.
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Affiliation(s)
- Qiang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Marcel Holyoak
- Department of Environmental Science and Policy, University of California, Davis, California, 95616, USA
| | - Eben Goodale
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Zhifa Liu
- Nanling National Nature Reserve, Shaoguan, 512727, China
| | - Yong Shen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jiajia Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Min Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Anqiang Dong
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Fasheng Zou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, 510260, China
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Macheriotou L, Rigaux A, Derycke S, Vanreusel A. Phylogenetic clustering and rarity imply risk of local species extinction in prospective deep-sea mining areas of the Clarion-Clipperton Fracture Zone. Proc Biol Sci 2020; 287:20192666. [PMID: 32228410 PMCID: PMC7209057 DOI: 10.1098/rspb.2019.2666] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
An understanding of the forces controlling community structure in the deep sea is essential at a time when its pristineness is threatened by polymetallic nodule mining. Because abiotically defined communities are more sensitive to environmental change, we applied occurrence- and phylogeny-based metrics to determine the importance of biotic versus abiotic structuring processes in nematodes, the most abundant invertebrate taxon of the Clarion–Clipperton Fracture Zone (CCFZ), an area targeted for mining. We investigated the prevalence of rarity and the explanatory power of environmental parameters with respect to phylogenetic diversity (PD). We found evidence for aggregation and phylogenetic clustering in nematode amplicon sequence variants (ASVs) and the dominant genus Acantholaimus, indicating the influence of environmental filtering, sympatric speciation, affinity for overlapping habitats and facilitation for community structure. PD was associated with abiotic variables such as total organic carbon, chloroplastic pigments equivalents and/or mud content, explaining up to 57% of the observed variability and providing further support of the prominence of environmental structuring forces. Rarity was high throughout, ranging from 64 to 75% unique ASVs. Communities defined by environmental filtering with a prevalence of rarity in the CCFZ suggest taxa of these nodule-bearing abyssal plains will be especially vulnerable to the risk of extinction brought about by the efforts to extract them.
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Affiliation(s)
- Lara Macheriotou
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Annelien Rigaux
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium.,Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Ankerstraat 1, 8400 Oostende, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281, Building S8, 9000 Ghent, Belgium
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Petruzzella A, da S S R Rodrigues TA, van Leeuwen CHA, de Assis Esteves F, Figueiredo-Barros MP, Bakker ES. Species identity and diversity effects on invasion resistance of tropical freshwater plant communities. Sci Rep 2020; 10:5626. [PMID: 32221401 PMCID: PMC7101304 DOI: 10.1038/s41598-020-62660-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/12/2020] [Indexed: 12/01/2022] Open
Abstract
Biotic resistance mediated by native plant diversity has long been hypothesized to reduce the success of invading plant species in terrestrial systems in temperate regions. However, still little is known about the mechanisms driving invasion patterns in other biomes or latitudes. We help to fill this gap by investigating how native plant community presence and diversity, and the presence of native phylogenetically closely related species to an invader, would affect invader Hydrilla verticillata establishment success in tropical freshwater submerged plant communities. The presence of a native community suppressed the growth of H. verticillata, but did not prevent its colonisation. Invader growth was negatively affected by native plant productivity, but independent of native species richness and phylogenetic relatedness to the invader. Native plant production was not related to native species richness in our study. We show that resistance in these tropical aquatic submerged plant communities is mainly driven by the presence and biomass of a native community independent of native species diversity. Our study illustrates that resistance provided by these tropical freshwater submerged plant communities to invasive species contrasts to resistance described for other ecosystems. This emphasizes the need to include understudied systems when predicting patterns of species invasiveness and ecosystem invasibility across biomes.
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Affiliation(s)
- Antonella Petruzzella
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands.
| | - Tauany A da S S R Rodrigues
- Laboratório de Limnologia, Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, 21 941-902, Cidade Universitária, Rio de Janeiro, Brazil
| | - Casper H A van Leeuwen
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands
| | - Francisco de Assis Esteves
- Laboratório de Limnologia, Departamento de Ecologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, 21 941-902, Cidade Universitária, Rio de Janeiro, Brazil
- Laboratório Integrado de Ecologia Aquática, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM/UFRJ), Av. São José Barreto 764, 27 965-045, São José do Barreto, Macaé, Rio de Janeiro, Brazil
| | - Marcos Paulo Figueiredo-Barros
- Laboratório Integrado de Ecologia Aquática, Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM/UFRJ), Av. São José Barreto 764, 27 965-045, São José do Barreto, Macaé, Rio de Janeiro, Brazil
| | - Elisabeth S Bakker
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands
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