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Article ; Online: Evolutionary diversity gradients in neotropical tree assemblages: New insights from Non‐Flooded Evergreen forests

Cupertino‐Eisenlohr, Mônica A. / Simon, Marcelo Fragomeni

Biotropica. 2023 Mar., v. 55, no. 2 p.454-466

2023

Abstract: We investigated spatial patterns of evolutionary diversity along Neotropical Non‐Flooded Evergreen Forests (NEF). We addressed the following questions: (i) What are the main NEF evolutionary groups? (ii) How evolutionary diversity varies across NEF ... ...

Abstract	We investigated spatial patterns of evolutionary diversity along Neotropical Non‐Flooded Evergreen Forests (NEF). We addressed the following questions: (i) What are the main NEF evolutionary groups? (ii) How evolutionary diversity varies across NEF environmental gradients? Based on a phylogeny of 1248 tree genera distributed over 1824 NEF assemblages, we examined the evolutionary differentiation using UPGMA and evopca. We measured lineage diversity (ses.PD) and structure (ses.MPD and ses.MNTD) and tested their response to environmental gradients using linear models. Phylogenetic dissimilarity segregated NEF into 12 evolutionary groups that largely confirm groups obtained in our previous work based on floristic similarity. However, one discrepancy was the amalgamation of Amazon and northern Atlantic Forest assemblages, while the southern Atlantic Forest remained an isolated group. Furthermore, Mesoamerica, which had been recognized as a single group, here split into six evolutionary groups. We found greater lineage diversity as altitude and latitude increased and temperature decreased. Evolutionary groups with the highest mean values of lineage diversity were those composed of Mesoamerican cloud forests, which harbor a mixture of tropical and temperate lineages representing a confluence of South and North American floras. We found that variations in phylogenetic diversity in NEF are primarily related to the coexistence of lineages of temperate and tropical climates in the mountain and nebular environments of NEF, indicating the strong contribution of extratropical niche conservatism in structuring evolutionary diversity.
Keywords	Neotropics ; altitude ; forests ; latitude ; niche conservatism ; phylogeny ; temperature ; trees ; Central America
Language	English
Dates of publication	2023-03
Size	p. 454-466.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2052061-X
ISSN	1744-7429 ; 0006-3606
ISSN (online)	1744-7429
ISSN	0006-3606
DOI	10.1111/btp.13199
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: TypeTaxonScript: sugarifying and enhancing data structures in biological systematics and biodiversity research.

Jordão, Lucas Sá Barreto / Morim, Marli Pires / Baumgratz, José Fernando A / Simon, Marcelo Fragomeni / Eppinghaus, André L C / Calfo, Vicente A

Biology methods & protocols

2024 Volume 9, Issue 1, Page(s) bpae017

Abstract: Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP ... ...

Abstract	Object-oriented programming (OOP) embodies a software development paradigm grounded in representing real-world entities as objects, facilitating a more efficient and structured modelling approach. In this article, we explore the synergy between OOP principles and the TypeScript (TS) programming language to create a JSON-formatted database designed for storing arrays of biological features. This fusion of technologies fosters a controlled and modular code script, streamlining the integration, manipulation, expansion, and analysis of biological data, all while enhancing syntax for improved human readability, such as through the use of dot notation. We advocate for biologists to embrace Git technology, akin to the practices of programmers and coders, for initiating versioned and collaborative projects. Leveraging the widely accessible and acclaimed IDE, Visual Studio Code, provides an additional advantage. Not only does it support running a Node.js environment, which is essential for running TS, but it also efficiently manages GitHub versioning. We provide a use case involving taxonomic data structure, focusing on angiosperm legume plants. This method is characterized by its simplicity, as the tools employed are both fully accessible and free of charge, and it is widely adopted by communities of professional programmers. Moreover, we are dedicated to facilitating practical implementation and comprehension through a comprehensive tutorial, a readily available pre-built database at GitHub, and a new package at npm.
Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Journal Article
ISSN	2396-8923
ISSN (online)	2396-8923
DOI	10.1093/biomethods/bpae017
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Article ; Online: From forest to savanna and back to forest: Evolutionary history of the genus Dimorphandra (Fabaceae).

Rocha, Vinicius Delgado da / Dal'Sasso, Thaís Carolina da Silva / Williams, Christina Cleo Vinson / Simon, Marcelo Fragomeni / Bueno, Marcelo Leandro / Oliveira, Luiz Orlando de

Journal of plant research

2024 Volume 137, Issue 3, Page(s) 377–393

Abstract: The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which ... ...

Abstract	The tree genus Dimorphandra (Fabaceae), which contains 26 species divided into three subgenera, was studied using DNA sequence data from six chloroplast genome regions (cpDNA) and the nuclear internal transcribed spacer (ITS). The analyses, which included Bayesian phylogenies and haplotype networks, ancestral area reconstructions, and ecological niche modeling, allowed for exploring the evolutionary history of Dimorphandra. Within the subgenus Phaneropsia, the cpDNA sequence data were more closely-related to species from the genus Mora, while the ITS sequence data displayed a closer phylogenetic relationship with the subgenus Pocillum. This incongruence may be due to incomplete lineage sorting associated with ancient polymorphisms. The Amazonian Dimophandra lineages were highly polymorphic and divergent, while those from the Cerrado and the Atlantic Forest had low levels of polymorphisms. The Amazon likely gave rise to the Dimophandra lineage that produced the Cerrado species, while a Cerrado lineage likely gave rise to the Atlantic Forest species. Habitat shifts were identified as a key factor in shaping the late evolutionary history of Dimorphandra.
MeSH term(s)	Phylogeny ; Fabaceae/genetics ; Fabaceae/classification ; Forests ; Grassland ; DNA, Chloroplast/genetics ; Haplotypes ; Biological Evolution ; Sequence Analysis, DNA ; Genome, Chloroplast/genetics ; Bayes Theorem ; Evolution, Molecular ; DNA, Plant/genetics ; Ecosystem
Chemical Substances	DNA, Chloroplast ; DNA, Plant
Language	English
Publishing date	2024-02-19
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2077362-6
ISSN	1618-0860 ; 0918-9440
ISSN (online)	1618-0860
ISSN	0918-9440
DOI	10.1007/s10265-024-01523-6
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Article ; Online: Eriocaulaceae: A new classification system based on morphological evolution and molecular evidence

Andrino, Caroline Oliveira / Costa, Fabiane Nepomuceno / Simon, Marcelo Fragomeni / Missagia, Rafaela Velloso / Sano, Paulo Takeo

TAXON. 2023 June, v. 72, no. 3 p.515-549

2023

Abstract: Paepalanthus, in its current sense, is the most diverse genus of Eriocaulaceae in the Neotropics, comprising about 400 species. Previous studies have consistently found that the genus is not monophyletic, also being morphologically heterogeneous and ... ...

Abstract	Paepalanthus, in its current sense, is the most diverse genus of Eriocaulaceae in the Neotropics, comprising about 400 species. Previous studies have consistently found that the genus is not monophyletic, also being morphologically heterogeneous and diagnosable by a set of homoplasies; thus, the current circumscription needs to be revised. The new classification proposed here uses a comprehensive phylogeny of Paepalanthus and closely related genera as a framework and an evaluation of a set of morphological characters using ancestral state reconstruction, which allowed the recognition of strongly supported clades with morphological diagnosability. We propose the recognition of 12 genera in the clade encompassing Paepalanthus and allied groups, including six new genera (Coracoralina, Floralia, Giuliettia, Gnomus, Hydriade, Nisius), two new statuses (Cryptanthella, Monosperma), the reestablishment of Actinocephalus, Lachnocaulon, and Tonina, and a recircumscription of Paepalanthus. In this new circumscription, Paepalanthus comprises 257 species, most of them restricted to the Brazilian campos rupestres. Among the proposed genera, nine have potential morphological synapomorphies, one has a restricted geographical distribution, and the other two can be recognized by a combination of characters. Newly generated seed morphology data is consistent within the different genera and plays an important role in their recognition. A total of 136 new combinations are hereby proposed. We provide a genus‐level identification key, as well as generic descriptions, diagnostic features, photos illustrating their morphological diversity, maps and notes on distribution, and lists of species by genus.
Keywords	Lachnocaulon ; Neotropics ; Paepalanthus ; geographical distribution ; monophyly ; seed morphology ; synapomorphy ; taxonomic keys
Language	English
Dates of publication	2023-06
Size	p. 515-549.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12915
Database	NAL-Catalogue (AGRICOLA)

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Article: Plant diversity conservation in an agricultural frontier in the Brazilian Cerrado

de Oliveira Santana, Jéssica Cauana / Simon, Marcelo Fragomeni

Biodiversity and conservation. 2022 Feb., v. 31, no. 2

2022

Abstract: The conversion of natural landscapes associated with agricultural activities is one of the major causes for the decline of biodiversity, especially in tropical regions. However, conservation planning within these regions is often hampered by insufficient ...

Abstract	The conversion of natural landscapes associated with agricultural activities is one of the major causes for the decline of biodiversity, especially in tropical regions. However, conservation planning within these regions is often hampered by insufficient biological data. In this work, we compiled plant diversity data for the agricultural frontier known as Matopiba. This is an area experiencing accelerated habitat loss. Although home to one of the largest remnants of natural vegetation in the Brazilian Cerrado biodiversity hotspot, only scant knowledge of its plant diversity exists. In total, we compiled 24,312 unique angiosperm records belonging to 139 families, 796 genera and 2,517 species. Occurrence data are very sparse. Approximately 39% of the region has < 0.1 record/km², and only two areas have more than 1 record/km². Rarefaction curves and a steady increase in new species discovery (27 new species from 2015–2020) indicate that knowledge of plant diversity in the study area is far from complete. Despite the significant proportion of collection gaps, our results suggest that the region’s flora is considerably rich, including 54 endemics and 38 threatened species. However, only 15% of the flora has been evaluated for conservation status. Only 28% of endemic and 53% of threatened species are reported to occur in protected areas. It is expected that this study will encourage a greater sampling effort to fill gaps in floristic knowledge and contribute data to support biodiversity conservation in a key region that is under high pressure by agricultural expansion.
Keywords	Angiospermae ; biodiversity conservation ; cerrado ; conservation status ; flora ; habitat destruction ; new species ; species diversity ; threatened species
Language	English
Dates of publication	2022-02
Size	p. 667-681.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	2000787-5
ISSN	1572-9710 ; 0960-3115
ISSN (online)	1572-9710
ISSN	0960-3115
DOI	10.1007/s10531-022-02356-2
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Article ; Online: Three New Species of Mimosa L. (Leguminosae) from the Brazilian Cerrado Hotspot of Biodiversity

Mendes, Thainara Policarpo / Simon, Marcelo Fragomeni / Silva, Marcos José da

Brittonia. 2022 Dec., v. 74, no. 4 p.361-380

2022

Abstract: Three new species of Mimosa endemic to the Brazilian Cerrado biodiversity hotspot are described and illustrated. Mimosa cavalcantina, M. gustavoi and M. venosa are assigned to subser. Polycephalae for having its diagnotic morphology, including unarmed ... ...

Abstract	Three new species of Mimosa endemic to the Brazilian Cerrado biodiversity hotspot are described and illustrated. Mimosa cavalcantina, M. gustavoi and M. venosa are assigned to subser. Polycephalae for having its diagnotic morphology, including unarmed branches, leaves with a pair of pinnae, a fimbriate paleaceous calyx, and filaments shortly monadelpous at the base. We summarize geographic distributions, habitats, phenology, and conservation status for each of the new species, compare them with morphologically similar congeners, and discuss their systematic positions.
Keywords	Mimosa ; biodiversity ; calyx ; cerrado ; conservation status ; new species ; phenology
Language	English
Dates of publication	2022-12
Size	p. 361-380.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	2052060-8
ISSN	1938-436X ; 0007-196X
ISSN (online)	1938-436X
ISSN	0007-196X
DOI	10.1007/s12228-022-09723-x
Database	NAL-Catalogue (AGRICOLA)

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Article: A New Species of Mimosa L. ser. Bipinnatae DC. (Leguminosae) from the Cerrado: Taxonomic and Phylogenetic Insights

Morales, Matías / Fortunato, Renée H / Simon, Marcelo Fragomeni

Plants. 2020 July 24, v. 9, no. 8

2020

Abstract: Mimosa carolina (Leguminosae), a new species from the Parque Nacional Chapada das Mesas, located in the northern limit of the Brazilian Cerrado, is described and illustrated. In addition, a phylogenetic reconstruction was performed to recover the ... ...

Abstract	Mimosa carolina (Leguminosae), a new species from the Parque Nacional Chapada das Mesas, located in the northern limit of the Brazilian Cerrado, is described and illustrated. In addition, a phylogenetic reconstruction was performed to recover the position of this species in relation to the main clades of the genus Mimosa. This new species is assigned to sect. Habbasia ser. Bipinnatae and exhibits relevant morphological differences with all described species of this series, most notably the prostate habit, glabrous stems, and absence of internal spicules. Our results indicate that this new entity is clearly nested in a strongly supported clade with other striated-corolla species of ser. Bipinnatae. Therefore, ser. Bipinnatae appears to be monophyletic, and a morphologically and ecologically cohesive group within Mimosa. An updated identification key for this series is provided.
Keywords	Mimosa ; cerrado ; monophyly ; new species ; scientific illustration ; stems ; taxon descriptions ; taxonomic keys
Language	English
Dates of publication	2020-0724
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants9080934
Database	NAL-Catalogue (AGRICOLA)

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Article: A New Species of

Morales, Matías / Fortunato, Renée H / Simon, Marcelo Fragomeni

Plants (Basel, Switzerland)

2020 Volume 9, Issue 8

Abstract: ... Mimosa ... ...

Abstract	Mimosa carolina
Language	English
Publishing date	2020-07-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants9080934
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Article ; Online: Mega-dams and extreme rainfall: Disentangling the drivers of extensive impacts of a large flooding event on Amazon Forests.

Oliveira, Washington Luis / Medeiros, Marcelo Brilhante / Moser, Pamela / Simon, Marcelo Fragomeni

PloS one

2021 Volume 16, Issue 2, Page(s) e0245991

Abstract: Extreme weather events and the presence of mega-hydroelectric dams, when combined, present an emerging threat to natural habitats in the Amazon region. To understand the magnitude of these impacts, we used remote sensing data to assess forest loss in ... ...

Abstract	Extreme weather events and the presence of mega-hydroelectric dams, when combined, present an emerging threat to natural habitats in the Amazon region. To understand the magnitude of these impacts, we used remote sensing data to assess forest loss in areas affected by the extreme 2014 flood in the entire Madeira River basin, the location of two mega-dams. In addition, forest plots (26 ha) were monitored between 2011 and 2015 (14,328 trees) in order to evaluate changes in tree mortality, aboveground biomass (AGB), species composition and community structure around the Jirau reservoir (distance between plots varies from 1 to 80 km). We showed that the mega-dams were the main driver of tree mortality in Madeira basin forests after the 2014 extreme flood. Forest loss in the areas surrounding the reservoirs was 56 km2 in Santo Antônio, 190 km2 in Jirau (7.4-9.2% of the forest cover before flooding), and 79.9% above that predicted in environmental impact assessments. We also show that climatic anomalies, albeit with much smaller impact than that created by the mega-dams, resulted in forest loss along different Madeira sub-basins not affected by dams (34-173 km2; 0.5-1.7%). The impact of flooding was greater in várzea and transitional forests, resulting in high rates of tree mortality (88-100%), AGB decrease (89-100%), and reduction of species richness (78-100%). Conversely, campinarana forests were more flood-tolerant with a slight decrease in species richness (6%) and similar AGB after flooding. Taking together satellite and field measurements, we estimate that the 2014 flood event in the Madeira basin resulted in 8.81-12.47 ∙ 106 tons of dead biomass. Environmental impact studies required for environmental licensing of mega-dams by governmental agencies should consider the increasing trend of climatic anomalies and the high vulnerability of different habitats to minimize the serious impacts of dams on Amazonian biodiversity and carbon stocks.
Language	English
Publishing date	2021-02-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0245991
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: New Species of Mimosa (Leguminosae) from Brazil

Barreto Jordão, Lucas Sá / Morim, Marli Pires / Simon, Marcelo Fragomeni / Dutra, Valquíria Ferreira / Baumgratz, José Fernando A.

Systematic botany. 2021 Aug. 11, v. 46, no. 2

2021

Abstract: Mimosa is a species-rich genus with about 600 species distributed mainly in the Neotropics. Mimosa is especially diverse in the Cerrado where the genus shows high levels of endemism, but it is also represented in the Caatinga (the Brazilian seasonally ... ...

Abstract	Mimosa is a species-rich genus with about 600 species distributed mainly in the Neotropics. Mimosa is especially diverse in the Cerrado where the genus shows high levels of endemism, but it is also represented in the Caatinga (the Brazilian seasonally dry vegetations). Four new species are described here, M. emaensis and M. sevilhae from the Cerrado, M. afranioi from the Caatinga, and M. robsonii from the Atlantic domain. We assessed their informal conservation status and two species would likely be categorized as Endangered (EN), one as Vulnerable (VU) to extinction, and one as Data Deficient (DD).
Keywords	Mimosa ; Neotropics ; caatinga ; cerrado ; conservation status ; extinction ; indigenous species ; new species ; Brazil
Language	English
Dates of publication	2021-0811
Size	p. 339-351.
Publishing place	American Society of Plant Toxonomists
Document type	Article
ZDB-ID	2052625-8
ISSN	1548-2324 ; 0363-6445
ISSN (online)	1548-2324
ISSN	0363-6445
DOI	10.1600/036364421X16231782047271
Database	NAL-Catalogue (AGRICOLA)

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