Biogeography and conservation status of the pineapple family (Bromeliaceae)

Zizka, Alexander; Azevedo, Josué A. R.; Leme, Elton M. C.; Neves, Beatriz; Costa, Andrea; Cáceres, Daniel; Zizka, Georg

doi:10.1111/ddi.13004

Cited by 55 publications

(52 citation statements)

References 73 publications

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“…The accuracy of the automated conservation assessment was in the same range as found by previous studies (Nic Lughadha et al 2019; Zizka, Azevedo, et al 2019). The similar accuracy of the raw and filtered dataset for the automated conservation assessment was surprising, in particular given the EOO and AOO reduction observed in the filtered dataset (Table 4) and the impact of errors on spatial analyses observed in previous studies (Gueta and Carmel 2016).…”

Section: Discussionsupporting

confidence: 84%

“…These methods approximate species’ range size, namely the Extent of Occurrence (EOO, which is the area of a convex hull polygon comprising all records of a species), the Area of Occupancy (AOO, which is the sum of the area actually occupied by a species, calculated based on a small-scale regular grid), and the number of locations for a preliminary conservation assessment following IUCN Criterion B (“Geographic range”). These methods have been used to propose preliminary global (Stévart et al 2019; Zizka, Azevedo, et al 2019) and regional (Schmidt et al 2017; Cosiaux et al 2018) Red List assessments. However, all metrics but especially EOO, are sensitive to individual records with erroneous coordinates.…”

Section: Introductionmentioning

confidence: 99%

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No one-size-fits-all solution to clean GBIF

Zizka

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Calvente

et al. 2020

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28Species occurrence records provide the basis for many biodiversity studies. They derive from geo-referenced 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 flagging and filtering are a scalable and reproducible means to identify potentially problematic records in datasets from public databases such as the Global Biodiversity Information Facility (GBIF; www.gbif.org). However, it is unclear how much data may be lost by filtering, whether the same tests should be applied across all taxonomic groups, and what is the effect of filtering for 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 animals, fungi, and plants, terrestrial and marine, downloaded from GBIF. We find that 29-90% of the records are potentially erroneous, with large variation across taxonomic groups. Tests for duplicated information, collection year, basis of record as well as urban areas and coordinates for terrestrial taxa in the sea or marine taxa on land have the greatest effect. While many flagged records might not be de facto erroneous, they could be overly imprecise and increase uncertainty in downstream analyses. Automated flagging 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 exploration of the meta-data associated with species records for biodiversity research. 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44Publicly available species distribution data have become a crucial resource in biodiversity research, including studies in 46 ecology, biogeography, systematics and conservation biology. In particular, the availability of digitized collections from 47 museums and herbaria, and citizen science observations has increased drastically over the last few years. As of today, 48 the largest public aggregator for geo-referenced species occurrences data, the Global Biodiversity Information Facility 49 (www.gbif.org), provides access to more than 1.3 billion geo-referenced occurrence records for species from across the 50 globe and the tree of life. 51A central challenge to the use of these publicly available species occurrence data in research are erroneous geographic 52 coordinates (Anderson et al. 2016). Errors mostly arise because public databases integrate records collected with 53 different methodologies in different places, at different times; often without centralized curation and only rudimentary 54 meta-data. For instance, erroneous coordinates caused by data-entry errors or automated geo-referencing from vague 55 locality descriptions are common (Maldonado et al. 2015; Yesson et al. 2007)...

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Section: Discussionsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

No one-size-fits-all solution to clean GBIF

Zizka

Carvalho

Calvente

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…These methods approximate species' range size, namely the Extent of Occurrence (EOO, which is the area of a convex hull polygon comprising all records of a species), the Area of Occupancy (AOO, which is the sum of the area actually occupied by a species, calculated based on a small-scale regular grid), and the number of locations for a preliminary conservation assessment following IUCN Criterion B (''Geographic range''). These methods have been used to propose preliminary global (Stévart et al, 2019;Zizka et al, 2020) and regional (Schmidt et al, 2017;Cosiaux et al, 2018) Red List assessments. However, all metrics, and especially EOO, are sensitive to individual records with problematic coordinates.…”

Section: Introductionmentioning

confidence: 99%

No one-size-fits-all solution to clean GBIF

Zizka

Carvalho

Calvente

et al. 2020

PeerJ

Self Cite

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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.

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“…To assess the environmental correlates of the genomic characters, 19 climatic variables were extracted from the WorldClim v1.4 database (Hijmans et al, 2005) downloaded at the 30 seconds resolution for all Bromelioideae species based on the recently published species distribution ranges (Zizka et al, 2020). The shape of the refined distributional polygons was used as a 'zonal feature' to extract values of each Bioclim variable for all species using ArcGIS v10.0.…”

Section: Data Analysesmentioning

confidence: 99%

Early Diverging and Core Bromelioideae (Bromeliaceae) Reveal Contrasting Patterns of Genome Size Evolution and Polyploidy

et al. 2020

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The subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein-Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.

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Biogeography and conservation status of the pineapple family (Bromeliaceae)

Cited by 55 publications

References 73 publications

No one-size-fits-all solution to clean GBIF

No one-size-fits-all solution to clean GBIF

No one-size-fits-all solution to clean GBIF

Early Diverging and Core Bromelioideae (Bromeliaceae) Reveal Contrasting Patterns of Genome Size Evolution and Polyploidy

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