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Article: A taxonomic dataset of preserved specimen occurrences of

Colli-Silva, Matheus / Richardson, James E / Pirani, José R

2023 Volume 11, Page(s) e99646

Abstract: Background: Species from the "cacao group" are traditionally allocated into two genera, : New information: Our dataset compiles 7975 records of preserved specimen collections found at herbaria. Records are from 18 species ... ...

Abstract	Background: Species from the "cacao group" are traditionally allocated into two genera, New information: Our dataset compiles 7975 records of preserved specimen collections found at herbaria. Records are from 18 species of
Language	English
Publishing date	2023-03-30
Publishing country	Bulgaria
Document type	Journal Article
ZDB-ID	2736709-5
ISSN	1314-2828
ISSN	1314-2828
DOI	10.3897/BDJ.11.e99646
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Current knowledge of the occurrence and distribution of Sapindales in Brazil: a data synthesis from the Brazilian Flora 2020 project

Colli-Silva, Matheus / Pirani, José Rubens

Revista brasileira de botânica. 2022 Mar., v. 45, no. 1

2022

Abstract: The Sapindales comprise one of the hallmark orders in the Neotropics, being an important component of forested and open formations, especially in Brazil. In recent decades, there have been many efforts made to unravel the Brazilian flora and its ... ...

Abstract	The Sapindales comprise one of the hallmark orders in the Neotropics, being an important component of forested and open formations, especially in Brazil. In recent decades, there have been many efforts made to unravel the Brazilian flora and its distribution; among them is the Brazilian Flora 2020 Project, the main goal of which was to produce updated monographs about Brazilian plant groups. In this work, we present a synthesis of the occurrence and distributions of species and genera of Sapindales in Brazil, noting species endemic to the country, as well as the prevalence of the order in Brazilian phytogeographic domains and vegetations. We have shown that Brazil has 1003 native species in 119 genera of six families of Sapindales, with 388 (43%) species endemic to the country, and the Rutaceae and Sapindaceae families being the richest in species, genera and endemics. Diverse species and life forms are found in virtually all vegetations and phytogeographic domains, but mostly in rainforests of the Amazonian and Atlantic Forest domains. Life forms vary greatly across different families, with a prevalence of lianas in Sapindaceae and of trees in Rutaceae. We discuss our results in light of the current patterns of the families and their assemblage in different vegetation and pytogeographic domains of Brazil.
Keywords	Neotropics ; Rutaceae ; Sapindaceae ; flora ; indigenous species ; phytogeography ; Brazil
Language	English
Dates of publication	2022-03
Size	p. 223-235.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	2686406-X
ISSN	1806-9959 ; 0100-8404
ISSN (online)	1806-9959
ISSN	0100-8404
DOI	10.1007/s40415-021-00739-3
Database	NAL-Catalogue (AGRICOLA)

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Article: Ayenia albiflora, (Malvaceae, Byttnerioideae) a new species from the Cerrado of Goiás, Central‐West Brazil

Colli‐Silva, Matheus / de Morais, Isa Lucia

Nordic journal of botany. 2022 May, v. 2022, no. 5

2022

Abstract: In this work, we describe a new species of Ayenia (Malvaceae, Byttnerioideae). Ayenia albiflora sp. nov. is known from the Cerrado areas of southern Goiás, Central‐West Brazil. It can be distinguished from its relatives by its outlying white bisexual ... ...

Abstract	In this work, we describe a new species of Ayenia (Malvaceae, Byttnerioideae). Ayenia albiflora sp. nov. is known from the Cerrado areas of southern Goiás, Central‐West Brazil. It can be distinguished from its relatives by its outlying white bisexual flowers and leaves with irregular dentate margin with obovate to subelliptic shape. A distribution map with known occurrence records, as well as comments on the ecology, morphological features and phenology of the species are provided. Moreover, we present an updated identification key of Ayenia species from Central‐West Brazil, distinguishing A. albiflora from its congeners.
Keywords	Malvaceae ; cerrado ; new species ; phenology ; taxonomic keys ; Brazil
Language	English
Dates of publication	2022-05
Publishing place	Blackwell Publishing Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2406507-9
ISSN	1756-1051 ; 0107-055X
ISSN (online)	1756-1051
ISSN	0107-055X
DOI	10.1111/njb.03562
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A taxonomic dataset of preserved specimen occurrences of Theobroma and Herrania (Malvaceae, Byttnerioideae) stored in 2020

Colli-Silva, Matheus / Richardson, J. E. / Pirani, José R.

Biodiversity Data Journal. 2023 Mar. 30, v. 11 p.e99646-

2023

Abstract: Species from the "cacao group" are traditionally allocated into two genera, Theobroma and Herrania (Malvaceae, Byttnerioideae), both groups of Neotropical species economically relevant, such as the cacao tree (Theobromacacao), which forms the source of ... ...

Abstract	Species from the "cacao group" are traditionally allocated into two genera, Theobroma and Herrania (Malvaceae, Byttnerioideae), both groups of Neotropical species economically relevant, such as the cacao tree (Theobromacacao), which forms the source of chocolate. This study aimed at compiling and describing a dataset of preserved specimen collections available in the Global Biodiversity Information Facility repository (GBIF) for Tropical Americas. Data were exhaustively revisited and analysed in terms of taxonomic identity, conditions of collection and georeferencing, all of which should enable downstream taxonomic, geographic and evolutionary analyses. Our dataset compiles 7975 records of preserved specimen collections found at herbaria. Records are from 18 species of Theobroma and 14 of Herrania, occurring in 60 countries or major territories, with two species endemic to a single country (H.kofanorum from Ecuador and H.laciniifolium from Colombia). Occurrence records are mostly restricted to the Amazon rainforest and species with more occurrence records are cupuí, T.subincanum (1535 records), followed by the cacao tree, T.cacao (1500 records), the latter having cultivated specimens in Africa, Asia and Oceania. In the case of the genus Herrania, H.nitida and H.purpurea are the species with the majority of occurrences (respectively, 431 and 273 records). Most of the botanical samples from these genera are found in American, Brazilian and Colombian collections, with a particular strength for American herbaria. We describe how occurrence records are spread spatially and temporally and highlight key field expeditions responsible for enhancing most of the knowledge of cacao and its wild relatives, especially in countries where they prevail, such as Colombia (with 29 species), Ecuador (23 species), Brazil (18 species) and Peru (15 species). Specifically, expeditions in these countries were led by American and European initiatives in conjunction with local funding in the mid-20ᵗʰ century. We emphasise how initiatives of such kind seems to have weakened in the 21ˢᵗ century and most of the collections of Theobroma and Herrania made afterwards are from various collectors that seek to resample specimens in already explored sites.
Keywords	Herrania ; Neotropics ; Theobroma cacao ; biodiversity ; chocolate ; data collection ; georeferencing ; Africa ; Amazonia ; Asia ; Brazil ; Colombia ; Ecuador ; Pacific Ocean Islands ; Peru ; flowering plants ; herbarium collections ; online repository
Language	English
Dates of publication	2023-0330
Publishing place	Pensoft Publishers
Document type	Article ; Online
ZDB-ID	2736709-5
ISSN	1314-2828
ISSN	1314-2828
DOI	10.3897/BDJ.11.e99646
Database	NAL-Catalogue (AGRICOLA)

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Article: Ecological niche models and point distribution data reveal a differential coverage of the cacao relatives (Malvaceae) in South American protected areas

Colli-Silva, Matheus / Pirani, José Rubens / Zizka, Alexander

Ecological informatics. 2022 July, v. 69

2022

Abstract: For many regions, such as in South America, it is unclear how well the existent protected areas network (PAs) covers different taxonomic groups and if there is a coverage bias of PAs towards certain biomes or species. Publicly available occurrence data ... ...

Abstract	For many regions, such as in South America, it is unclear how well the existent protected areas network (PAs) covers different taxonomic groups and if there is a coverage bias of PAs towards certain biomes or species. Publicly available occurrence data along with ecological niche models might help to overcome this gap and to quantify the coverage of taxa by PAs ensuring an unbiased distribution of conservation effort. Here, we use a published occurrence database of 271 species from the cacao family (Malvaceae) to explore how South American PAs cover species with different distribution, abundance, and threat status. Furthermore, we compared the performance of online databases, expert knowledge, and modelled species distributions in estimating species coverage in PAs. We found 79 species from our survey (29% of the total) lack any record inside South American PAs and that 20 out of 23 species potentially threatened with extinction are not covered by PAs. The area covered by South American PAs was low across biomes, except for Amazonia, which had a relative high PA coverage, but little information on species distribution within PA available. Also, raw georeferenced occurrence data were underestimating the number of species in PAs, and projections from ecological niche models were more prone to overestimating the number of species represented within PAs. We discuss that the protection of South American flora in heterogeneous environments demand for specific strategies tailored to particular biomes, including collecting specimens inside PAs in less collected areas, and the delimitation of areas for protection in more known areas.
Keywords	Malvaceae ; databases ; expert opinion ; extinction ; flora ; geographical distribution ; georeferencing ; issues and policy ; niches ; surveys ; Amazonia ; South America
Language	English
Dates of publication	2022-07
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2212016-6
ISSN	1878-0512 ; 1574-9541
ISSN (online)	1878-0512
ISSN	1574-9541
DOI	10.1016/j.ecoinf.2022.101668
Database	NAL-Catalogue (AGRICOLA)

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Article: Estimating bioregions and undercollected areas in South America by revisiting Byttnerioideae, Helicteroideae and Sterculioideae (Malvaceae) occurrence data

Colli-Silva, Matheus / Pirani, José Rubens

Flora. 2020 Oct., v. 271

2020

Abstract: Revisiting biogeographical patterns is the first step towards fully assessing the natural history and conservation of particular lineages, an important effort in species-rich groups from heterogeneous or undercollected areas, such as South American ... ...

Abstract	Revisiting biogeographical patterns is the first step towards fully assessing the natural history and conservation of particular lineages, an important effort in species-rich groups from heterogeneous or undercollected areas, such as South American Malvaceae. Here, we compile, synthetize and discuss a manually revisited distribution database built for species of three subfamilies of Malvaceae—Byttnerioideae, Helicteroideae and Sterculioideae—from South America. Our database was assembled from vouchers publicly available in online repositories and from an extensive literature survey. We retrieved 14,528 records of 271 species in 11 genera, 231 (85%) endemic to South America. Different species are indicative of different bioregions, collection efforts for the groups are heterogeneous within South America, and the Amazon region is the area with highest levels of biasing effects. Occurrence records are widespread throughout South America, and most species are centered in open seasonally dry formations, especially in the Brazilian Cerrado, Caatinga and the Chaco. Furthermore, we found secondary centers of species richness in the Northwestern region of South America, in the Andean portions of Colombia, Ecuador and Peru, as well as in the Southern portion of the Brazilian Atlantic Forest. The Amazon region—the most undercollected area of South America for the groups—also shows some remarkable records, namely from arborescent genera of Byttnerioideae (Theobroma and Herrania) and species of Sterculioideae. Occurrence maps of species richness, a full list of revisited records and a summary of records per species were presented and discussed considering known biogeographical patterns for plants in the Neotropical region.
Keywords	Herrania ; Neotropics ; Theobroma ; caatinga ; cerrado ; databases ; flora ; forests ; geographical distribution ; natural history ; species richness ; surveys ; Amazonia ; Andes region ; Colombia ; Ecuador ; Peru
Language	English
Dates of publication	2020-10
Publishing place	Elsevier GmbH
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	5580-3
ISSN	0367-2530 ; 0373-6490
ISSN	0367-2530 ; 0373-6490
DOI	10.1016/j.flora.2020.151688
Database	NAL-Catalogue (AGRICOLA)

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Article: Outstanding plant endemism levels strongly support the recognition of campo rupestre provinces in mountaintops of eastern South America

Colli‐Silva, Matheus / Vasconcelos, Thais N. C / Pirani, José Rubens

Journal of biogeography. 2019 Aug., v. 46, no. 8

2019

Abstract: AIM: The Brazilian campo rupestre is a vegetation associated to ancient mountaintops in eastern South America, spread mainly over disjunct areas of the Espinhaço Range and the Chapada dos Veadeiros. These areas hold outstanding levels of plant diversity ... ...

Abstract	AIM: The Brazilian campo rupestre is a vegetation associated to ancient mountaintops in eastern South America, spread mainly over disjunct areas of the Espinhaço Range and the Chapada dos Veadeiros. These areas hold outstanding levels of plant diversity and endemism, but despite their uniqueness they have been neglected in recent bioregionalizations for the Neotropical region. Given their particular levels of species richness and endemism, we here test the recognition of these as distinct bioregions within the Chacoan dominion. LOCATION: Mountaintops of eastern South America. METHODS: We listed 1,748 angiosperm species endemic to the campo rupestre of the Espinhaço Range and Chapada dos Veadeiros regions, based on the data gathered from the Brazilian Flora 2020 Project. We extracted all occurrence information available from GBIF (the Global Biodiversity Information Facility) for such list and also for a polygon gathering all the study area, including information from adjacent vegetations. Data went through standard cleaning procedures and a network clustering analysis was performed to delimitate the boundaries of the new bioregions. RESULTS: Our data strongly support the recognition of two distinct bioregions along the Espinhaço Range, but none in the Chapada dos Veadeiros. Given their high levels of endemism and singularity within the Chacoan dominion, we formalize two provinces associated to campo rupestre in the Espinhaço Range, naming them as “Chapada Diamantina” and “Southern Espinhaço” provinces. Within the latter province, three districts are also recognized, based on this and previous studies: “Diamantina Plateau”, “Grão‐Mogol” and “Iron Quadrangle” districts. MAIN CONCLUSIONS: The formalization of new and previously described bioregions highlights the campo rupestre as a vegetation harbouring outstanding levels of species richness and endemism in South America, contributing to a better understanding of biogeographical patterns in the Neotropics. Also, as we follow the International Code of Area Nomenclature as a device to standardize recognition of bioregions, this shall facilitate further biogeographical and conservation studies in these areas. Further assessments with new and revisited data are needed to enable minor scale bioregionalization within the Chacoan dominion.
Keywords	Angiospermae ; Neotropics ; cleaning ; cluster analysis ; flora ; geographical distribution ; indigenous species ; mountains ; species richness ; vegetation ; South America
Language	English
Dates of publication	2019-08
Size	p. 1723-1733.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	188963-1
ISSN	0305-0270
ISSN	0305-0270
DOI	10.1111/jbi.13585
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: People-inspired names remain valuable.

Antonelli, Alexandre / Farooq, Harith / Colli-Silva, Matheus / Araújo, João P M / Freitas, André V L / Gardner, Elliot M / Grace, Olwen / Gu, Shiran / Marline, Lovanomenjanahary / Nesbitt, Mark / Niskanen, Tuula / Onana, Jean Michel / Pérez-Escobar, Oscar A / Taylor, Charlotte / Knapp, Sandra

Nature ecology & evolution

2023 Volume 7, Issue 8, Page(s) 1161–1162

Language	English
Publishing date	2023-06-19
Publishing country	England
Document type	Letter
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-023-02108-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Evaluating shortfalls and spatial accuracy of biodiversity documentation in the Atlantic Forest, the most diverse and threatened Brazilian phytogeographic domain

Colli‐Silva, Matheus / Reginato, Marcelo / Cabral, Andressa / Forzza, Rafaela Campostrini / Pirani, José Rubens / Vasconcelos, Thais N. da C.

Taxon. 2020 June, v. 69, no. 3

2020

Abstract: Digital accessible knowledge of biodiversity data is an increasingly important source of information in studies of biogeography and conservation. These databases can also reveal temporal, spatial and taxonomical gaps in biodiversity documentation, even ... ...

Abstract	Digital accessible knowledge of biodiversity data is an increasingly important source of information in studies of biogeography and conservation. These databases can also reveal temporal, spatial and taxonomical gaps in biodiversity documentation, even in areas that have been intensively studied and from where accurate species lists are available. Therefore, revealing these gaps may help allocating collecting efforts, conservation priorities and strategies for improving database curation. Here, we evaluate potential shortfalls for flowering plants in a tropical hotspot, the Brazilian Atlantic Forest, by cross‐referencing two online repositories of biodiversity data (the Global Biodiversity Information Facility – GBIF – and the Brazilian Flora 2020 floristic database – BFG). We aimed to evaluate the congruence between those repositories, highlighting tendencies in current documentation for this area. We found that from the 7220 reported flowering plant species endemics to the Atlantic Forest, 1573 (22%) have no valid spatial data in GBIF, and 75% of all of the 605,951 records do not present valid spatial information. Most of the missing information is related to species known only from few and old collections with absent or inaccurately georeferenced data. This lack of information may cause a large impact in spatial studies, especially for rare and threatened species. Nevertheless, our analysis also shows that spatial information for the filtered data is highly congruent between GBIF and BFG data, indicating relatively high availability of quality data in large repositories after standard and automatized cleaning procedures. Still, good practices to decrease the impact of losing data are recommended, including more investment in field collections, targeting poorly known species and returning cleaned spatial datasets to online repositories after taxonomic revisions.
Keywords	biodiversity ; databases ; flora ; forests ; georeferencing ; information sources ; phytogeography ; spatial data ; threatened species
Language	English
Dates of publication	2020-06
Size	p. 567-577.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	204216-2
ISSN	0040-0262
ISSN	0040-0262
DOI	10.1002/tax.12239
Database	NAL-Catalogue (AGRICOLA)

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Article: No one-size-fits-all solution to clean GBIF.

Zizka, Alexander / Antunes Carvalho, Fernanda / Calvente, Alice / Rocio Baez-Lizarazo, Mabel / Cabral, Andressa / Coelho, Jéssica Fernanda Ramos / Colli-Silva, Matheus / Fantinati, Mariana Ramos / Fernandes, Moabe F / Ferreira-Araújo, Thais / Gondim Lambert Moreira, Fernanda / Santos, Nathália Michellyda Cunha / Santos, Tiago Andrade Borges / Dos Santos-Costa, Renata Clicia / Serrano, Filipe C / Alves da Silva, Ana Paula / de Souza Soares, Arthur / Cavalcante de Souza, Paolla Gabryelle / Calisto Tomaz, Eduardo /

Vale, Valéria Fonseca / Vieira, Tiago Luiz / Antonelli, Alexandre

PeerJ

2020 Volume 8, Page(s) e9916

Abstract: Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the ... ...

Abstract	Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25-90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.
Language	English
Publishing date	2020-09-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.9916
Database	MEDical Literature Analysis and Retrieval System OnLINE

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