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 https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/

• 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. https://doi.org/10.1371/journal.pone.0287957

• 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

29-Feb-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.   

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Shawn Laffan

03-Feb-2024

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

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).

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Shawn Laffan

03-Feb-2024

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

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.  

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Shawn Laffan

03-Feb-2024

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Biodiverse now calculates the CANAPE super class

Since version 4.3, Biodiverse has calculated and plotted the CANAPE results when the relevant calculations have been run. 

However, it did not calculate the super class when first implemented. Now it does.

From version 5, Biodiverse calculates all CANAPE classes when a randomisation is run for an analysis that includes phylogenetic endemism and relative phylogenetic endemism.    

Note that the CANAPE classed are only updated after at least one randomisation iteration has been run.  If you have an existing randomisation then you can run one more iteration to trigger the calculation.  Otherwise you can run a new randomisation with the same settings.  This should not take long for most analyses, assuming they are consistent with the sizes of data sets in existing publications.     

If you are wondering why it was not plotted in the first place, it was largely because the plotting system needed some re-engineering to allow for additional legend labels.  This was done when the z-score and p-rank plotting was implemented, a little while after the initial CANAPE plotting.  

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Shawn Laffan

02-Dec-2023

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Biodiverse 4.3 has been released

 

Biodiverse version 4.3 has now been released.  

Versions for Windows, Mac and Linux (Ubuntu) are available and can be accessed via https://github.com/shawnlaffan/biodiverse/wiki/Downloads

Installation instructions are at https://github.com/shawnlaffan/biodiverse/wiki/Installation

This release contains a small number of bug fixes and improved functionality. 

For the full list of issues and changes leading to the 4.3 release, see https://github.com/shawnlaffan/biodiverse/milestone/21

Main changes:

GUI:

z-score plotting has been fixed (colours were reversed). Issue 857.

Randomisations

The p-rank calculations now generate ranks for all defined values. The GUI also now colours the values, similar to the z-scores. Issue 856. More details in the blog post.

Spatial conditions

The sp_points_in_same_poly_shape condition is now faster when any points do not intersect any polygons. See commit 3ca2703.

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Shawn Laffan

01-May-2023

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions 

Changes to randomisation results - the p-rank data

 

Randomisations in Biodiverse produce a range of outputs.  These are kept in a range of lists, differing by name (see the help system).  

One of the lists that is generated in the p-ranks.  This is essentially the same as the P_ values in the main randomisation lists but where the low values account for ties so one can be sure the values represent the relative ranking of the observed value against those generated from the randomised data.  For example, the significance of a low value should account for any ties.

The p-ranks were implemented a few years versions ago and are detailed in this blog post.  Due to how the plotting was set up at the time, only values in the outer 10% of the distribution were retained. This helped understand which groups contained significant results without a major update to the display system but in the end was probably confusing.  Now that the z-score plotting has been implemented the system has the infrastructure to handle the full range of values.  

So what has changed?  

Two things: the calculation of values and how they are plotted.  

Note that the set of cells that can be regarded as significant using the standard alpha threshold of 0.05 for high or low values is unchanged.  All that has changed is the number of cells with defined values and how they are displayed in the GUI.  

The calculation   

Put simply, all values are now retained.  Any "P_" value less than 0.5 accounts to the number of ties.  Expressed as pseudocode it is:

if P_index > 0.5

  p_rank = P_index 

else 

  p_rank = ((C_index + T_index) / Q_index)  

where "index" is whichever index is being compared at the time.  

This makes post-hoc calculation of compound indices like CANAPE easier (although remember that Biodiverse now does that for you).  

The display

The addition of the z-score plotting means that the infrastructure for the plotting is in place so it was not too difficult to re-use it to instead display percentile classes.  This is applied to the p-score lists by default.  

Compare the two plots below and consider which is easier to work with.  

The p-rank plotting in Biodiverse version 4.2 and earlier works, but it is difficult to see which cells are in specific percentile bands.  For example which of these cells is in the outer 5%?  

Indices in the p-rank lists are now plotted as percentile classes.  Compare with the plot above.   

As with other plots, the coloured cells can be exported as RGB geotiffs to display in a GIS or other plotting system.  

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Shawn Laffan

27-Apr-2023

For more details about Biodiverse, see http://shawnlaffan.github.io/biodiverse/  

For a list of some of the analyses Biodiverse has been used for, see https://github.com/shawnlaffan/biodiverse/wiki/PublicationsList 

You can also join the Biodiverse-users mailing list at https://groups.google.com/group/Biodiverse-users or start a discussion at https://github.com/shawnlaffan/biodiverse/discussions