Thursday 29 February 2024

Publications using Biodiverse in 2023

2024 is moving quickly, so here is a list of publications from 2023 that used Biodiverse.

If you want to see the full list (211 at the time of writing), then go to

For more details about Biodiverse, see

  • Aragón-Parada, J., Carrillo-Reyes, P., Rodríguez, A., Munguía-Lino, G., Salinas-Rodríguez, M. M. and De-Nova, J. A. (2023) Spatial phylogenetics of the flora in the Sierra Madre del Sur, Mexico: Evolutionary puzzles in tropical mountains. Journal of Biogeography, 50, 1679-1691.

  • Copilaș-Ciocianu, D., Sidorov, D., & Šidagytė-Copilas, E. (2023). Global distribution and diversity of alien Ponto-Caspian amphipods. Biological Invasions, 25, 179-195.

  • de Pedro, D., Ceccarelli, F.S., Vandame, R. et al. (2023) Congruence between species richness and phylogenetic diversity in North America for the bee genus Diadasia (Hymenoptera: Apidae). Biodiversity and Conservation, 32, 4445–4459.

  • Dlamini, W.M.D. and Loffler, L. (2023). Tree Species Diversity and Richness Patterns Reveal High Priority Areas for Conservation in Eswatini. In: Dhyani, S., Adhikari, D., Dasgupta, R., Kadaverugu, R. (eds) Ecosystem and Species Habitat Modeling for Conservation and Restoration. Springer, Singapore.

  • Erst, A.S., Baasanmunkh, S., Tsegmed, Z. et al. (2023) Hotspot and conservation gap analysis of endemic vascular plants in the Altai Mountain Country based on a new global conservation assessment. Global Ecology and Conservation, 47, e02647

  • Fernandes, N.B.G., Moraes, A.M. and Milward-de-Azevedo, M.A. (2023) Diversity of the Passiflora L. in the Serra do Mar ecoregion and the relationships with environmental gradients, South and Southeast, Brazil. Acta Botanica Brasilia, 37, e20220314.

  • Flores-Argüelles, A., López-Ferrari, A.R., & Espejo-Serna, A. (2023). Geographic distribution and endemism of Bromeliaceae from the Western Sierra-Coast region of Jalisco, Mexico. Botanical Sciences, 101, 527-543.

  • Flores-Tolentino, M. et al. (2023). Delimitación geográfica y florística de la provincia fisiográfica de la Depresión del Balsas, México, con énfasis en el bosque tropical estacionalmente seco. Revista mexicana de biodiversidad, 94, e944985.

  • Francisco-Gutiérrez, A., Eduardo Ruiz-Sanchez, E. and Lira-Noriega, A. (2023) Biogeography and conservation assessments of the species of Lamourouxia (Orobanchaceae). Acta Botanica Mexicana 130: e2213.

  • González-Orozco, C.E. (2023) Unveiling evolutionary cradles and museums of flowering plants in a neotropical biodiversity hotspot. Royal Society Open Science, 10230917230917.

  • González-Orozco, C.E., Diaz-Giraldo, R.A. and Rodriguez-Castañeda, C. (2023) An early warning for better planning of agricultural expansion and biodiversity conservation in the Orinoco high plains of Colombia. Frontiers in Sustainable Food Systems, 7.

  • González-Orozco, C., Osorio-Guarín, J., & Yockteng, R. (2023). Phylogenetic diversity of cacao (Theobroma cacao L.) genotypes in Colombia. Plant Genetic Resources, 20, 203-214.

  • González-Orozco, C.E. & Parra-Quijano, M. (2023) Comparing species and evolutionary diversity metrics to inform conservation. Diversity and Distributions, 29, 224-231.

  • González-Orozco, C. E., Reyes-Herrera, P. H., Sosa, C. C., Torres, R. T., Manrique-Carpintero, N. C., Lasso-Paredes, Z., Cerón-Souza, I. and Yockteng, R. (in press). Wild relatives of potato (Solanum L. sec. Petota) poorly sampled and unprotected in Colombia. Crop Science.

  • Guo, WY., Serra-Diaz, J.M., Eiserhardt, W.L. et al. (2023) Climate change and land use threaten global hotspots of phylogenetic endemism for trees. Nature Communications, 14, 6950.

  • Mardones, D. and Scherson, R.A. (2023) Hotspots within a hotspot: evolutionary measures unveil interesting biogeographic patterns in threatened coastal forests in Chile. Botanical Journal of the Linnean Society, 202, 433–448.

  • McCurry, M.R., Park, T., Coombs, E.J. Hart, L.J., Laffan, S. (2023) Latitudinal gradients in the skull shape and assemblage structure of delphinoid cetaceans. Biological Journal of the Linnean Society, 138, 470-480.

  • Miller, J.T., Prentice, E., Bui, E.N., Knerr, N., Mishler, B.D., Schmidt-Lebuhn, A.N., González-Orozco, C.E., Laffan, S. W. (2023). Banksia (Proteaceae) contains less phylogenetic diversity than expected in Southwestern Australia. Journal of Systematics and Evolution, 61, 957-966.

  • Molina-Paniagua, M.E., Alves de Melo, P.H., Ramírez-Barahona, S., Monro, A.K., Burelo-Ramos, C.M., Gómez-Domínguez, H., et al. (2023) How diverse are the mountain karst forests of Mexico? PLoS ONE 18, e0292352.

  • Nicolau, G.K. and Edwards, S. (2023) Diversity and endemism of Southern African Gekkonids linked with the escarpment has implications for conservation priorities. Diversity, 15, 306.

  • Ortiz-Brunel J.P., Ochoterena H., Moore M.J., Aragón-Parada J., Flores J., Munguía-Lino G., Rodríguez A., Salinas-Rodríguez M.M. and Flores-Olvera H. (2023) Patterns of Richness and Endemism in the Gypsicolous Flora of Mexico. Diversity, 15, 522.

  • Ramírez-Verdugo, P., Tapia, A., Forest, F. and Scherson, R.A. (2023) Evolutionary diversity of the endemic genera of the vascular flora of Chile and its implications for conservation. PLoS ONE 18(7): e0287957.

  • Ruiz-Sanchez, E., Munguía-Lino, G., Pianissola, E.M., Ely, F. and Clark, L.G. (2023) Richness and endemism in Chusquea subg. Swallenochloa (Poaceae), a Neotropical subgenus adapted to temperate conditions. Phytotaxa, 609, 180-194.

  • Villaseñor, J. L., Ortiz, E., & Hernández-Flores, M. M. (2023). The vascular plant species endemic or nearly endemic to Puebla, Mexico. Botanical Sciences, 101, 1207-1221.

  • Wang, C., Zhu, S., Jiang, X., Chen, S., Xiao, Y., Zhao, Y., Yan, Y. and Wen, Y. (2023) Spatio-temporal variation of species richness and phylogenetic diversity patterns for spring ephemeral plants in northern China. Global Ecology and Conservation, 48, e02752.

  • Ye, C. et al. (2023) Geographical distribution and conservation strategy of national key protected wild plants of China. iScience, 26, 107364.

  • Zhang, H., Chen, S.-C., Bonser, S.P., Hitchcock, T., & Moles, A.T. (2023). Factors that shape large-scale gradients in clonality. Journal of Biogeography, 50, 827-837

  • Zhou, R., Ci, X., Hu, J., Zhang, X., Cao, G., Xiao, J., Liu, Z., Li, L., Thornhill, A.H., Conran, J.G. and Li, J. (2023) Transitional areas of vegetation as biodiversity hotspots evidenced by multifaceted biodiversity analysis of a dominant group in Chinese evergreen broad-leaved forests. Ecological Indicators, 147, 110001

Shawn Laffan


Saturday 3 February 2024

Map side menu: The tree plot controls are now a separate submenu, and some new features

From version 5 of Biodiverse the tree plot controls in the left side menu are now their own submenu.  This greatly simplifies the interface.

The displayed tree can now be exported, including the colours used when plotting the tree.  Previously the colours were not stored so this was not possible.  To export the colours corresponding to a specific cell then right click on that cell to fix the colouring in place.  This stops any further updates until another cell is clicked on.  The interface itself is unchanged, including the options to export the colours and an RGB geotiff of the spatial plot.  

In addition, there are several new plotting options that allow one to plot using equal and range weighted branch lengths.  


It is now possible to plot the tree using normal branch lengths, depth and also equal branch length and range weighted.  

The equal branch length tree is the alternate tree in the CANAPE protocol

The range weighted tree can be used to understand how PE works.  

The ranged weighted equal branch length tree can be used to understand the RPE index used in CANAPE.   


Shawn Laffan


For more details about Biodiverse, see  

For a list of some of the analyses Biodiverse has been used for, see 

You can also join the Biodiverse-users mailing list at or start a discussion at 

Tree panels: colour the tree using any list from spatial outputs across the project

It has long been possible to colour the tree branches in the spatial tab.  However, it was only possible to use a list from the spatial analysis being plotted.  

From version 5 the interface has been changed to enable selection of any list from spatial outputs across the project.  Where before the system had a simple drop down list, it is now a menu with submenus for each basedata and then each of its spatial outputs. 

The tree colour list selection is now a menu that allows users to choose any list across all spatial outputs in the project 

As with most widgets in the GUI, the menu entries are described in the tooltip.  That text is duplicated below.  

The first (default) option shows the paths connecting the labels in the neighbour sets used for the analysis. When there is one such set all branches are coloured blue. When there are two such sets blue denotes branches only in the first set, red denotes those only in the second set, and black denotes those in both. From these one can see the turnover of branches between the groups (cells) in each neighbour set.

The next set of menu options are list indices in the spatial output that belongs to this tab.  The remainder are lists across other spatial outputs in the project, organised by their basedata objects.  These are in the same order as in the Outputs tab.  Basedatas and outputs with no list indices are not shown.

If a branch is not in the list then it is highlighted using a default colour (usually black).  If the selected output has no labels that are also on the tree then no highlighting is done (all branches remain black).

Right clicking on a group (cell) fixes the highlighting in place, stopping changes to the branch colouring as the mouse is hovered over other groups.  This allows the tree to be exported with the current colouring (another new option in version 5).


Shawn Laffan


For more details about Biodiverse, see  

For a list of some of the analyses Biodiverse has been used for, see 

You can also join the Biodiverse-users mailing list at or start a discussion at 

Trimming basedatas has been generalised

It has long been possible to trim the basedata labels to keep only those that match either the selected tree or selected matrix.  

From Version 5 (actually 4.99_002 if you like development versions) it is possible to trim using a different basedata.  The interface has also been generalised in the process.    

There's not much to it, so here are some screenshots to demonstrate the process.  

Generalised trimming is accessed from the basedata menu

It has the usual interface where one can specify a new name.  "Trimming a clone" ensures it operates on a copy.  "Delete matching" allows one to invert the trim, i.e. if one wants to keep only the labels that do not match,

Any of the basedatas, trees or matrices in the project can be selected to use as the label source.  


Shawn Laffan


For more details about Biodiverse, see  

For a list of some of the analyses Biodiverse has been used for, see 

You can also join the Biodiverse-users mailing list at or start a discussion at