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Bartholomew DC, Hayward R, Burslem DFRP, Bittencourt PRL, Chapman D, Bin Suis MAF, Nilus R, O'Brien MJ, Reynolds G, Rowland L, Banin LF, Dent D. Bornean tropical forests recovering from logging at risk of regeneration failure. Glob Chang Biol 2024; 30:e17209. [PMID: 38469989 DOI: 10.1111/gcb.17209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 03/13/2024]
Abstract
Active restoration through silvicultural treatments (enrichment planting, cutting climbers and liberation thinning) is considered an important intervention in logged forests. However, its ability to enhance regeneration is key for long-term recovery of logged forests, which remains poorly understood, particularly for the production and survival of seedlings in subsequent generations. To understand the long-term impacts of logging and restoration we tracked the diversity, survival and traits of seedlings that germinated immediately after a mast fruiting in North Borneo in unlogged and logged forests 30-35 years after logging. We monitored 5119 seedlings from germination for ~1.5 years across a mixed landscape of unlogged forests (ULs), naturally regenerating logged forests (NR) and actively restored logged forests via rehabilitative silvicultural treatments (AR), 15-27 years after restoration. We measured 14 leaf, root and biomass allocation traits on 399 seedlings from 15 species. Soon after fruiting, UL and AR forests had higher seedling densities than NR forest, but survival was the lowest in AR forests in the first 6 months. Community composition differed among forest types; AR and NR forests had lower species richness and lower evenness than UL forests by 5-6 months post-mast but did not differ between them. Differences in community composition altered community-weighted mean trait values across forest types, with higher root biomass allocation in NR relative to UL forest. Traits influenced mortality ~3 months post-mast, with more acquisitive traits and relative aboveground investment favoured in AR forests relative to UL forests. Our findings of reduced seedling survival and diversity suggest long time lags in post-logging recruitment, particularly for some taxa. Active restoration of logged forests recovers initial seedling production, but elevated mortality in AR forests lowers the efficacy of active restoration to enhance recruitment or diversity of seedling communities. This suggests current active restoration practices may fail to overcome barriers to regeneration in logged forests, which may drive long-term changes in future forest plant communities.
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Affiliation(s)
- David C Bartholomew
- School of Geography, University of Exeter, Exeter, UK
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Botanic Gardens Conservation International, Richmond, UK
| | - Robin Hayward
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
- School of Earth and Environment, University of Leeds, Leeds, UK
| | | | | | - Daniel Chapman
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | | | - Reuben Nilus
- Forest Research Centre Sepilok, Sandakan, Malaysia
| | - Michael J O'Brien
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Almería, Spain
| | - Glen Reynolds
- SE Asia Rainforest Research Partnership, Kota Kinabalu, Sabah, Malaysia
| | - Lucy Rowland
- School of Geography, University of Exeter, Exeter, UK
| | | | - Daisy Dent
- Smithsonian Tropical Research Institute, Balboa, Panama
- Department of Environmental Systems Science, ETH, Zürich, Switzerland
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Brainard SH, Sanders DM, Bruna T, Shu S, Dawson JC. The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus. Plant Biotechnol J 2024; 22:472-483. [PMID: 37870930 PMCID: PMC10826982 DOI: 10.1111/pbi.14199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome-scale assemblies for this species using the accessions 'Rush' and 'Winkler'. Genomes were assembled using HiFi PacBio reads and Arima Hi-C data, and Oxford Nanopore reads and a high-density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for 'Rush' and 'Winkler', respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. 'Rush' has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while 'Winkler' had corresponding scores of 96.9 and 96.5, indicating high-quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana, as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high-density SNP marker sets from genotyping-by-sequencing data using 1343 C. americana, C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self-incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self-incompatibility in Corylus.
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Affiliation(s)
- Scott H. Brainard
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Dean M. Sanders
- University of Wisconsin Biotechnology CenterUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Tomas Bruna
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Julie C. Dawson
- Department of Plant and Agroecosystem SciencesUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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Cunha Neto IL, Hall BT, Lanba AR, Blosenski JD, Onyenedum JG. Laser ablation tomography (LATscan) as a new tool for anatomical studies of woody plants. New Phytol 2023; 239:429-444. [PMID: 36811411 DOI: 10.1111/nph.18831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/09/2023] [Indexed: 06/02/2023]
Abstract
Traditionally, botanists study plant anatomy by carefully sectioning samples, histological staining to highlight tissues of interests, then imaging slides under light microscopy. This approach generates significant details; however, this workflow is laborious, particularly in woody vines (lianas) with heterogeneous anatomies, and ultimately yields two-dimensional (2D) images. Laser ablation tomography (LATscan) is a high-throughput imaging system that yields hundreds of images per minute. This method has proven useful for studying the structure of delicate plant tissues; however, its utility in understanding the structure of woody tissues is underexplored. We report LATscan-derived anatomical data from several stems of lianas (c. 20 mm) of seven species and compare these results with those obtained through traditional anatomical techniques. LATscan successfully allows the description of tissue composition by differentiating cell type, size, and shape, but also permits the recognition of distinct cell wall composition (e.g. lignin, suberin, cellulose) based on differential fluorescent signals on unstained samples. LATscan generate high-quality 2D images and 3D reconstructions of woody plant samples; therefore, this new technology is useful for both qualitative and quantitative analyses. This high-throughput imaging technology has the potential to bolster phenotyping of vegetative and reproductive anatomy, wood anatomy, and other biological systems.
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Affiliation(s)
- Israel L Cunha Neto
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, NY, 14853, Ithaca, USA
| | - Benjamin T Hall
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
| | - Asheesh R Lanba
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
- Department of Engineering, University of Southern Maine, 37 College Ave., Gorham, ME, 04038, USA
| | - Joshua D Blosenski
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
| | - Joyce G Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, NY, 14853, Ithaca, USA
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Sreekar R, Katabuchi M, Nakamura A, Corlett RT, Slik JWF, Fletcher C, He F, Weiblen GD, Shen G, Xu H, Sun IF, Cao K, Ma K, Chang LW, Cao M, Jiang M, Gunatilleke IAUN, Ong P, Yap S, Gunatilleke CVS, Novotny V, Brockelman WY, Xiang W, Mi X, Li X, Wang X, Qiao X, Li Y, Tan S, Condit R, Harrison RD, Koh LP. Spatial scale changes the relationship between beta diversity, species richness and latitude. R Soc Open Sci 2018; 5:181168. [PMID: 30839691 PMCID: PMC6170539 DOI: 10.1098/rsos.181168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/22/2018] [Indexed: 06/09/2023]
Abstract
The relationship between β-diversity and latitude still remains to be a core question in ecology because of the lack of consensus between studies. One hypothesis for the lack of consensus between studies is that spatial scale changes the relationship between latitude and β-diversity. Here, we test this hypothesis using tree data from 15 large-scale forest plots (greater than or equal to 15 ha, diameter at breast height ≥ 1 cm) across a latitudinal gradient (3-30o) in the Asia-Pacific region. We found that the observed β-diversity decreased with increasing latitude when sampling local tree communities at small spatial scale (grain size ≤0.1 ha), but the observed β-diversity did not change with latitude when sampling at large spatial scales (greater than or equal to 0.25 ha). Differences in latitudinal β-diversity gradients across spatial scales were caused by pooled species richness (γ-diversity), which influenced observed β-diversity values at small spatial scales, but not at large spatial scales. Therefore, spatial scale changes the relationship between β-diversity, γ-diversity and latitude, and improving sample representativeness avoids the γ-dependence of β-diversity.
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Affiliation(s)
- Rachakonda Sreekar
- School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia,Australia
| | - Masatoshi Katabuchi
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - Akihiro Nakamura
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, People's Republic of China
| | - Richard T. Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Menglun, Yunnan 666303, People's Republic of China
| | - J. W. Ferry Slik
- Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, Brunei Darussalam
| | - Christine Fletcher
- Forestry and Environment Division, Forest Research Institute Malaysia, Kepong, Selangor 52109, Malaysia
| | - Fangliang He
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, CanadaT6G 2G7
| | - George D. Weiblen
- Bell Museum and Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
| | - Guochun Shen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Han Xu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Tianhe, Guangzhou 510520, People's Republic of China
| | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien 97401, Taiwan, Republic of China
| | - Ke Cao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Li-Wan Chang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan, Republic of China
| | - Min Cao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, People's Republic of China
| | - Mingxi Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, People's Republic of China
| | | | - Perry Ong
- Institute of Biology, University of the Philippines, Diliman, Philippines
| | - Sandra Yap
- Institute of Arts and Sciences, Far Eastern University, Manila, Philippines
| | | | - Vojtech Novotny
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences and Faculty of Science, University of South Bohemia, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
- New Guinea Binatang Research Center, PO Box 604, Madang, Papua New Guinea
| | - Warren Y. Brockelman
- BIOTEC, National Science and Technology Development Agency, 113 Science Park, Klongluang, Pathum Thani 12120, Thailand
| | - Wusheng Xiang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin 541006, People's Republic of China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Xiankun Li
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin 541006, People's Republic of China
| | - Xihua Wang
- Tiantong National Forest Ecosystem Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, People's Republic of China
| | - Xiujuan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, People's Republic of China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Tianhe, Guangzhou 510520, People's Republic of China
| | - Sylvester Tan
- Center for Tropical Forest Science – Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Richard Condit
- Center for Tropical Forest Science – Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Rhett D. Harrison
- Agroforestry Centre, East and Southern Africa Region, 13 Elm Road, Woodlands, Lusaka, Zambia
| | - Lian Pin Koh
- School of Biological Sciences, University of Adelaide, Adelaide 5005, South Australia,Australia
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Krishnadas M, Comita LS. Influence of soil pathogens on early regeneration success of tropical trees varies between forest edge and interior. Oecologia 2017; 186:259-268. [PMID: 29134399 DOI: 10.1007/s00442-017-4006-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/07/2017] [Indexed: 11/25/2022]
Abstract
Soil fungi are key mediators of negative density-dependent mortality in seeds and seedlings, and the ability to withstand pathogens in the shaded understory of closed-canopy forests could reinforce light gradient partitioning by tree species. For four species of tropical rainforest trees-two shade-tolerant and two shade-intolerant-we conducted a field experiment to examine the interactive effects of fungal pathogens, light, and seed density on germination and early seedling establishment. In a fully factorial design, seeds were sown into 1 m2 plots containing soil collected from underneath conspecific adult trees, with plots assigned to forest edge (high light) or shaded understory, high or low density, and fungicide or no fungicide application. We monitored total seed germination and final seedling survival over 15 weeks. Shade-intolerant species were strongly constrained by light; their seedlings survived only at the edge. Fungicide application significantly improved seedling emergence and/or survival for three of the four focal species. There were no significant interactions between fungicide and seed density, suggesting that pathogen spread with increased aggregation of seeds and seedlings did not contribute to pathogen-mediated mortality. Two species experienced significant edge-fungicide interactions, but fungicide effects in edge vs. interior forest varied with species and recruitment stage. Our results suggest that changes to plant-pathogen interactions could affect plant recruitment in human-impacted forests subject to fragmentation and edge-effects.
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Affiliation(s)
- Meghna Krishnadas
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA.
| | - Liza S Comita
- School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT, 06511, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancón, Panama
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