Building combined MRP-matrices with BuM, an automated web-tool

Hammoud, Muhsen; Góis, João Paulo; Santos, Daubian; Sampronha, Stephanie; Santos, Charles Morphy D.

doi:10.11646/zootaxa.4567.2.11

Cited by 5 publications

(2 citation statements)

References 4 publications

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“…After uploading a text file with the input area cladograms, iSAMBA generates the MRP‐combined matrix (cf. Hammoud et al, 2019; Santos et al, 2021), making it available to download in “.nex” and “.ss” files format. The MRP‐combined matrix can be analysed in any software that performs parsimony analysis such as TNT (Goloboff & Catalano, 2016) or Mesquite (Maddison & Maddison, 2019) (STEP 4).…”

Section: Implementing the Methods Through Isambamentioning

confidence: 99%

SAMBA: Super area‐cladogram after resolving multiple biogeographical ambiguities

Santos

Sampronha

Hammoud

et al. 2023

Journal of Biogeography

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Aim: Cladistic biogeography is all about congruence: when individual area cladograms coincide, they result in a general area cladogram that reveals shared history. However, the complexities of the natural world hamper the reconstruction of fully solved biogeographical patterns. Herein, we present SAMBA (super area-cladogram after resolving multiple biogeographical ambiguities), a pattern-based method combining supertrees and area cladograms to depict the relationships among areas. We also present a prototypical implementation of SAMBA as a web-based framework named iSAMBA. Location: Global.Taxon: Any taxon can be analysed with SAMBA.Methods: SAMBA is based on phylogenetic supertrees, a technique that combines previously calculated phylogenetic trees to produce a general area cladogram representing conciliatory and non-ambiguous patterns of relationships. In our method, the input topologies are individual area cladograms. SAMBA is implemented through a web-based framework named iSAMBA. We analysed a theoretical and a real scenario to compare SAMBA with primary Brooks parsimony analysis (BPA), component analysis, three area statement analysis (TAS) and the transparent method.Results: SAMBA produces area cladograms that converge with the actual history of fragmentations of both hypothetical and real scenarios used as examples of implementation of the method. Primary BPA, component analysis, TAS and the transparent method are much more affected by the "biogeographical noise" (e.g. multiple areas in a single terminal, paralogies and missing areas) than SAMBA.Main Conclusions: SAMBA results in more informative general area cladograms than other pattern-based biogeographical methods. SAMBA reveals shared patterns of biotic distribution without generating multiple unreliable area cladograms. The main advantage of SAMBA is the simplicity of using a single technique to extract biogeographical information from individual area cladograms and combine them to depict a non-ambiguous general pattern of relationships among areas.

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Section: Implementing the Methods Through Isambamentioning

confidence: 99%

SAMBA: Super area‐cladogram after resolving multiple biogeographical ambiguities

Santos

Sampronha

Hammoud

et al. 2023

Journal of Biogeography

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“…These databases represent a great optimization of the efforts made by distinct projects, as they will allow the continuity in the use of generated data. In addition, a few projects were involved with the development of computational tools, such as those presented by Hirakama et al ( 2009), Hammoud et al (2019aHammoud et al ( , 2019b and Santos & Fuhlendorf (2019). Tools of this type can offer new perspectives and analytical facilities that were previously not possible to be performed.…”

Section: Databasesmentioning

confidence: 99%

The contribution of the BIOTA/FAPESP Program to the advancement of the knowledge on terrestrial invertebrates

et al. 2022

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The variability of the organisms living in a given area constitute what is referred to as biodiversity, one of nature’s fundamental properties, responsible for the balance and stability of ecosystems. The loss of biodiversity has been of great concern to scientists, especially because of the role played by human activities in this regard, able to lead to irreversible circumstances. The São Paulo Research Foundation (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP) plays a major role in supporting research efforts in the most diverse branches of science. In the late 1990´s, FAPESP launched a major program to promote research on biodiversity, named BIOTA/FAPESP. So far, this program has financed the conduction of 26 projects, involving research activities in most of Brazil, while focusing mainly the State of São Paulo. These projects have generated about 1140 publications in peer-reviewed journals of high standard, providing relevant information, including the original description of 1187 species and 76 genera, the complementary description of 350 species, as well as a number of inventory works, biological studies, etc. The program has also been instrumental in the establishment or adequacy of research facilities and training of new taxonomists. Most extensively studied groups of terrestrial invertebrates include Insecta of the orders Hymenoptera, Lepidoptera and Diptera, and Arachnida of the subclasses Araneae and Acari. Distinct projects have also contributed to the detection of organisms potentially useful as biological control agents and in the determination of maps of major interest for the establishment of public policies. In the future, priority groups for study should include the Annelida and the Nematoda, for the potential both have as beneficial organisms, or for the potential some Nematoda have as organisms harmful to plants and animals.

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Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework

Hammoud

Santos

Góis

2022

Journal of Computational Biology

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Building combined MRP-matrices with BuM, an automated web-tool

Cited by 5 publications

References 4 publications

SAMBA: Super area‐cladogram after resolving multiple biogeographical ambiguities

SAMBA: Super area‐cladogram after resolving multiple biogeographical ambiguities

The contribution of the BIOTA/FAPESP Program to the advancement of the knowledge on terrestrial invertebrates

Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework

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