The Community Ecology and Conservation Group (CEC) recently hosted a highly engaging workshop, “Introduction to Bioinformatics and Omics Data Analysis,” from 10th to 14th February 2025 at the Xishuangbanna Tropical Botanical Garden. The event brought together European trainers, students, and professionals from China, all keen to explore the dynamic field of bioinformatics and its applications in omics data analysis.

The workshop aimed to equip participants with foundational knowledge and practical skills for handling large-scale biological datasets generated by genomics and transcriptomics. Over five intensive days, attendees learned essential tools, algorithms, and software used in bioinformatics, including hands-on sessions focused on data processing, visualisation, and interpretation.

Led by Dr. Guillem Ylla, head of the Laboratory of Bioinformatics and Genome Biology at Jagiellonian University (Kraków, Poland), the workshop featured interactive lectures and guided practical exercises. Dr. Ylla was supported by his postdoctoral researcher, Dr. Tomasz Gaczorek, who assisted with hands-on exercises. Key topics included an introduction to NGS data analysis and transcriptomics, de novo genome assembly (conducted by Dr. Evgenii Baiakhmetov, a special research assistant at CEC), population genomics (GWAS and SNP calling), and opportunities for direct interaction with the trainers.

Professor Kyle Tomlinson, one of the organisers, emphasised the workshop’s significance: “Bioinformatics is at the heart of modern biology, enabling us to decode complex omics data and drive scientific discovery. This programme fosters capacity-building and collaboration among young scientists.”

Participants praised the comprehensive curriculum and supportive environment, noting how the workshop empowered them to address their research challenges more effectively. Many expressed enthusiasm for applying their new skills to projects spanning biodiversity conservation and rapid speciation.

As the CEC continues to advance interdisciplinary science through cutting-edge approaches, this workshop highlights its commitment to fostering scientific innovation. Plans to expand future iterations of the programme are underway, ensuring accessibility to a broader audience.

R.K. Chaturvedi , Anshuman Tripathi, Rajiv Pandey , A.S. Raghubansi , J.S. Singh. Assessment of habitat features modulated carbon sequestration strategies for drought management in tropical dry forest fragments. Science of the Total Environment (2024). https://doi.org/10.1016/j.scitotenv.2024.175703

Abstract

Habitat features, such as species diversity, functional diversity, tree size, disturbances and fragment sizes have differential impacts on carbon (C) storage and C-sequestration in forest ecosystems. Present study attempted to understand the tree strategies for modulating C-sequestration capacity across tropical dry forest fragments with variable edge distances. We evaluated the differences between drought strategies (i.e., drought avoiding and drought tolerant) for variations in stem density, relative growth rate (RGR), C-storage and C-sequestration, species diversity, functional diversity, tree size and disturbance indicators along edge distance gradient, besides analyzed the differences between drought strategies for responses of C-storage and C-sequestration to variations in species diversity, functional diversity, tree size and disturbance indicators. Various traits and functional indices were analyzed using standard statistical techniques. For total trees and for the two drought strategies, generalized linear modeling results showed a significant decline in stem density, RGR, C-stock, C-sequestration, species diversity, functional diversity and tree size indicators, while a considerable increase in disturbance indicators, along decreasing edge distance across the fragments. The drought strategies exhibited a high degree of variation in the slope of associations for above variables with edge distance across fragments. For predicting C-sequestration, structural equation modeling results showed highly significant influence of functional diversity indicators for drought avoiding strategy, while species diversity indicators were strongly significant for drought tolerant strategy. Moreover, fire index and drought index were critical predictors for C-sequestration for drought avoiding and drought tolerant strategies, respectively. This study provide inputs to understand the largely ignored processes of C-storage and C-sequestration in fragmented forests, which are currently prevalent due to heavy anthropogenic pressures. Our findings are useful for forest managers to understand vegetation responses to interactions of species diversity, functional diversity, tree size and disturbance indicators, for predicting the stability of larger fragments and for planning restoration of smaller fragments.

For more details on papers published from this group, click here.

Anest, A., Bouchenak-Khelladi, Y., Charles-Dominique, T., Felix, F., Yves, C., Gareth, P. H., Olivier, M., Kyle, W. T., Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01649-4

Abstract

Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants.

For more details on papers published from this group, click here.

We are currently seeking to fill TWO POSTDOC POSITIONS in our lab, the Community Ecology & Conservation Group, at Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. The research considers the importance of small forest fragments in long-term resilience of vertebrate-dispersed tree species in a tropical forest landscape, Xishuangbanna, Southwest China, for which we have just received significant research grant support.


Project Background
Most forest fragments are small, and there is an ongoing debate as to whether they can sustain local sub-populations of trees, and whether they can contribute to species population stability in the landscape, by providing stepping stones between larger fragments. The problem is made more complex by the fact that vertebrate-dispersed tree species depend on vertebrates of different sizes. Large vertebrate-dispersed species are considered to be especially vulnerable because hunting has extirpated or suppressed their dominant dispersers, and the ability of secondary dispersers to functionally replace them is unclear.

In this study, we seek to understand the fate of several tree species with different vertebrate-dispersal modes in small fragments that lie between larger fragments. We are already using disperser assessments and seed fate analyses to understand recruitment success of the tree species in each fragment.


We are now seeking candidates to:
(1) run population genetics analyses in the fragments to understand the genetic health of the sub-populations and whether genetic exchange between fragments still contributes to genetic diversity in new recruits.
(2) record population dynamics of all size classes of trees in the fragments, and integrate the population genetics work and the juvenile recruitment work to understand long-term fate of the tree species using integral projection modelling techniques.

Fully trained support staff are on hand in the research group to aid with fieldwork.

Postdocs receive an annual salary (gross) of at least 200,000 RMB, with annual increments possible, subject to satisfactory progress. Accommodation is provided by the institute for a very nominal fee.

Applicants should have relevant educational experience, in either forest ecology, population genetics, or systems modelling. They should also be in good physical condition as the forest fragment terrain is variable. Candidates who pass initial assessment by the PI will need to pass an online panel interview before formal approval by the institute.

Expressions of interest, should be emailed to Professor Kyle Tomlinson (kyle.tomlinson@xtbg.org.cn), and should include an indication of which research topics you are interested in applying for, what relevant experience you have to support your application, and a full CV to back the expression of interest.

More information about the research group can be found at: https://communityecologyconservation.com/

Yang, J., Fan, H., He, Y., Wang, G., Cao, M. and Swenson, N.G., (2024). Functional genomics and co‐occurrence in a diverse tropical tree genus: The roles of drought‐and defence‐related genes. Journal of Ecology. https://doi.org/10.1111/1365-2745.14255

Abstract

1. Tropical tree communities are among the most diverse in the world. A small number of genera often disproportionately contribute to this diversity. How so many species from a single genus can co-occur represents a major outstanding question in biology. Niche differences are likely to play a major role in promoting congeneric diversity, but the mechanisms of interest are often not well-characterized by the set of functional traits generally measured by ecologists.
2. To address this knowledge gap, we used a functional genomic approach to investigate the mechanisms of co-occurrence in the hyper-diverse genus Ficus. Our study focused on over 800 genes related to drought and defence, providing detailed information on how these genes may contribute to the diversity of Ficus species.
3. We find widespread and consistent evidence of the importance of defence gene dissimilarity in co-occurring species, providing genetic support for what would be expected under the Janzen-Connell mechanism. We also find that drought-related gene sequence similarity is related to Ficus co-occurrence, indicating that similar responses to drought promote co-occurrence.
4. Synthesis. We provide the first detailed functional genomic evidence of how drought- and defence-related genes simultaneously contribute to the local co-occurrence in a hyper-diverse genus. Our results demonstrate the potential of community transcriptomics to identify the drivers of species co-occurrence in hyper-diverse tropical tree genera.

For more details on papers published from this group, click here.

Chaturvedi, R.K., Pandey, S.K., Tripathi, A., Goparaju, L., Raghubanshi, A.S., Singh, J.S., (2024). Variations in the plasticity of functional traits indicate the differential impact of abiotic and biotic factors on the structure and growth of trees in tropical dry forest fragments. Frontiers in Plant Science.  https://doi.org/10.3389/fpls.2023.1181293

Abstract

Abiotic and biotic factors have considerable impact on the plasticity of plant functional traits, which influences forest structure and productivity; however, their inter-relationships have not been quantified for fragmented tropical dry forest (TDF) ecosystems. We asked the following questions: (1) what are the variations in the plasticity of functional traits due to soil moisture availability in TDF fragments? (2) what are the roles of soil nutrients and forest disturbances in influencing variations in the plasticity of functional traits in the TDF fragments? and (3) how do the variations in the plasticity of functional traits influence the structure and productivity of TDF fragments? Based on linear mixed-effects results, we observed significant variations among tree species for soil moisture content (SMC) under the canopy and selected functional traits across forest fragments. We categorized tree species across fragments by principal component analysis (PCA) and hierarchical clustering on principal components (HCPC) analyses into three functional types, viz., low wood density high deciduous (LWHD), high wood density medium deciduous (HWMD), and high wood density low deciduous (HWLD). Assemblage of functional traits suggested that the LWHD functional type exhibits a drought-avoiding strategy, whereas HWMD and HWLD adopt a drought-tolerant strategy. Our study showed that the variations in functional trait plasticity and the structural attributes of trees in the three functional types exhibit contrasting affinity with SMC, soil nutrients, and disturbances, although the LWHD functional type was comparatively more influenced by soil resources and disturbances compared to HWMD and HWLD along the declining SMC and edge distance gradients. Plasticity in functional traits for the LWHD functional type exhibited greater variations in traits associated with the conservation of water and resources, whereas for HWMD and HWLD, the traits exhibiting greater plasticity were linked with higher productivity and water transport. The cumulative influence of SMC, disturbances, and functional trait variations was also visible in the relative abundance of functional types in large and small sized fragments. Our analysis further revealed the critical differences in the responses of functional trait plasticity of the coexisting tree species in TDF, which suggests that important deciduous endemic species with drought-avoiding strategies might be prone to strategic exclusion under expected rises in anthropogenic disturbances, habitat fragmentation, and resource limitations.

For more details on papers published from this group, click here.

This is a paper published in Nature and co-authored by Dr. Kyle W. Tomlinson, the head of the group.

Cooper, D.L.M., Lewis, S.L., Sullivan, M.J.P. et al. Consistent patterns of common species across tropical tree communities. Nature (2024). https://doi.org/10.1038/s41586-023-06820-z

Consistent patterns of common species across tropical tree communities

Abstract

Trees structure the Earth’s most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth’s 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories⁷, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world’s most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees.

For more details on papers published from this group, click here.

Maurin, O., Anest, A., Forest, F., Turner, I., Barrett, R. L., Cowan, R. C., Wang, L., Tomlinson, K. W., & Charles-Dominique, T. (2023). Drift in the tropics: Phylogenetics and biogeographical patterns in Combretaceae. Global Ecology and Biogeography, 00, 1–13. https://doi.org/10.1111/geb.13737

Abstract

Aim

The aim of this study was to further advance our understanding of the species-rich, and ecologically important angiosperm family Combretaceae to provide new insights into their evolutionary history. We assessed phylogenetic relationships in the family using target capture data and produced a dated phylogenetic tree to assess fruit dispersal modes and patterns of distribution.

Location

Tropical and subtropical regions.

Time Period

Cretaceous to present.

Major Taxa Studied

Family Combretaceae is a member of the rosid clade and comprises 10 genera and more than 500 species, predominantly assigned to genera Combretum and Terminalia, and occurring on all continents and in a wide range of ecosystems.

Methods

We use a target capture approach and the Angiosperms353 universal probes to reconstruct a robust dated phylogenetic tree for the family. This phylogenetic framework, combined with seed dispersal traits, biome data and biogeographic ranges, allows the reconstruction of the biogeographical history of the group.

Results

Ancestral range reconstructions suggest a Gondwanan origin (Africa/South America), with several intercontinental dispersals within the family and few transitions between biomes. Relative abundance of fruit dispersal types differed by both continent and biome. However, intercontinental colonizations were only significantly enhanced by water dispersal (drift fruit), and there was no evidence that seed dispersal modes influenced biome shifts.

Main Conclusions

Our analysis reveals a paradox as drift fruit greatly enhanced dispersal distances at intercontinental scale but did not affect the strong biome conservatism observed.

For more details on papers published from this group, click here.

Quibod MNRM, Gelin U, van Langevelde F, Tomlinson KW*. 2023. Diet-specific responses of skull traits to moisture gradients in bovids and cervids. Linnean Society Journal for Zoological Research. DOI: 10.1093/zoolinnean/zlad068

Abstract

Feeding efficiency of mammalian herbivores is associated with skull traits known to differ between feeding guilds. As climate is known to affect the architecture and functional traits of plants, skull morphology may change as plant traits change along climate gradients. We tested whether skull traits of more than 70% of the extant bovid and cervid species are related to aridity, and whether these relationships differ across feeding guilds (browser, grazer, mixed feeder). We used muzzle width to represent food ingestion and masseteric fossa length to represent oral processing. For the models without phylogeny, both muzzle width and masseteric fossa length increased towards wetter climates for grazers, but not for mixed feeders or browsers. These patterns suggest that grazer diets may change more dramatically across aridity gradients than the other two groups, possibly linked to changes in both the architecture and toughness of grasses. In models accounting for phylogeny, no changes in either trait across aridity gradient were found, which appeared to be due to subfamily differentiation along the aridity gradient. Our results suggest that deeper insights into the evolution of herbivore skulls may be achieved by using quantified diet data to directly test plant trait effects on skull morphology.

For more details on papers published from this group, click here.

Congratulations to Theo Lefebvre, Jan Sher, and Ninya Quibod who successfully defended their PhD dissertations and will graduate from their PhD degrees!

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