Relationships between species

Genomic data are increasingly applied to infer evolutionary relationships among species, supporting the development of robust and predictive classifications. 

DNA-level variation contains the evolutionary history of a species, but also a great deal of noise.

We are working to develop cost-effective means of discovering the signal and producing evolutionary trees which come as close as possible to the true story of how groups lineages evolved. This is vital for producing a true classification and for understanding evolution.

Revealing relationships

DNA-level variation contains the evolutionary history of a species, but also a great deal of noise.

We are working to develop cost-effective means of discovering the signal and producing evolutionary trees which come as close as possible to the true story of how lineages evolved. This is vital for producing a true classification and for understanding evolution.

We are currently using target capture to increase species discrimination and phylogenetic resolution in the closely related and highly emblematic conifer genus Araucaria from New Caledonia, where 70% of the 20 accepted Araucaria species are endemic.

We are also using target capture of DNA extracted from both silica gel-dried and herbarium samples, combined with traditional taxonomy, to investigate evolutionary relationships at different scales - among genera (e.g., in the subfamily Bombacoideae (Malvaceae), and in the Marchantiopsida, or complex thalloid liverworts) and among species, for example in the recently evolved (< 10 million years old) but highly diverse (> 300 spp) tropical tree genus Inga (Leguminosae).
Understanding species boundaries

We have used a wide range of genome data to resolve species boundaries and inter-specific relationships in large plant groups from centres of biodiversity such as the Hengduan Mountains, China, Seasonally Dry Tropical Forests in the Neotropics and the Cerrado savanna in Brazil.

We use raw sequences, ‘skims’ of genomes and assembled plastid genomes to reveal whether the evolutionary processes of these key groups are associated with climate history, ecological, orogenic and geological processes.
Making genomic data accessible

We are working to make it easy to access and work with data we’ve generated over many years with different technologies.

We are generating metadata-rich databases and pipelines to allow them to be found, accessed, documented and analysed (i.e., following the FAIR principles) easily for taxonomic, evolutionary or conservation studies.

RBGE's bioinformatics and data management website

Key Publications

Schley, Rowan J., Rosalía Piñeiro, James A. Nicholls, Flávia Fonseca Pezzini, Audrey Farbos, Gwilym P. Lewis, Jens J. Ringelberg et al. "Rampant Reticulation in a Rapid Radiation of Tropical Trees-Insights from Inga (Fabaceae)." Systematic biology (2025): https://doi.org/10.1093/sysbio/syaf027

Nicholls, James A., Jens J. Ringelberg, Kyle G. Dexter, Oriane Loiseau, Graham N. Stone, Phyllis D. Coley, Colin E. Hughes et al. "Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia." Proceedings B 292, no. 2039 (2025): 20241559. https://doi.org/10.1098/rspb.2024.1559

Chen, Yiqing, Lina Dong, Huiqin Yi, Catherine Kidner, and Ming Kang. Genomic divergence and mutational load in the Begonia masoniana complex from limestone karsts. Plant Diversity (2024). https://doi.org/10.1016/j.pld.2024.04.001

Clugston, J.A., Ruhsam, M., Kenicer, G.J., Henwood, M., Milne, R. and Nagalingum, N.S., 2022. Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. Conservation Genetics, 23(3), pp.449-465. https://doi.org/10.1007/s10592-022-01428-8

Yi, Huiqin, Shiyong Dong, Lihua Yang, Jing Wang, Catherine Kidner, and Ming Kang. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Molecular phylogenetics and evolution 184 (2023): 107801. https://doi.org/10.1016/j.ympev.2023.107801

Fernandes, M.F., Lewis, G.P., Vatanparast, M. Pezzini, F.F., Brown, M.J,M., Queiroz, L.P., Cardoso, D., Pennington, R.T. Knowledge gaps in legume diversity and distribution and prospects for future research. Brazilian Journal of Botany 48, 8 (2025). https://doi.org/10.1007/s40415-024-01051-6

Pezzini, Flávia Fonseca, Giada Ferrari, Laura L. Forrest, Michelle L. Hart, Kanae Nishii, and Catherine A. Kidner. Target capture and genome skimming for plant diversity studies. Applications in Plant Sciences 11, no. 4 (2023): e11537. https://doi.org/10.1002/aps3.11537

Phang, A., Pezzini, F.F., Burslem, D.F.R.P., Khew, G.S., Middleton, D.J., Ruhsam, M., Wilkie, P. Target capture sequencing for phylogenomic and population studies in the Southeast Asian genus Palaquium (Sapotaceae), Botanical Journal of the Linnean Society, Volume 203, Issue 2, October 2023, Pages 134–147, https://doi.org/10.1093/botlinnean/boad022

Phang, A., Niissalo, M., Ruhsam, M., Pezzini, F.F., Neo, W.L., Burslem, D.F.R.P., Middleton, D.J., Wilkie, P., Khew, G.S. Genetic erosion in a tropical tree species demonstrates the need to conserve wide-ranging germplasm amid extreme habitat fragmentation. Biodivers Conserv 33, 2527–2548 (2024). https://doi.org/10.1007/s10531-024-02870-5

Mo ZQ, J Wang, M MÖLLER, JBJ Yang, LM Gao (2023) Phylogenetic relationships and next-generation barcodes in the genus Torreya reveal a high proportion of misidentified cultivated plants. International Journal of Molecular Sciences 2023: 24, 13216. https://doi.org/10.3390/ijms241713216

Wang J, CN Fu, ZQ Mo, M MÖLLER, JB Yang, ZR Yang, DZ Li, LM Gao (2022). Testing the complete plastome for species discrimination, cryptic species discovery and phylogenetic resolution in Cephalotaxus (Cephalotaxaceae). Frontiers in Plants Science 13: 768810. https://doi.org/10.3389/fpls.2022.768810

Ogutcen E, C Christe, K Nishii, N Salamin, M MÖLLER, M Perret (2021). Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Molecular Phylogenetics and Evolution 157, e107068. https://doi.org/10.1016/j.ympev.2021.107068

Relationships between species

Revealing relationships

Understanding species boundaries

Making genomic data accessible

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