| 1. |
- Abarenkov, Kessy, et al.
(author)
-
Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
-
Journal article (peer-reviewed)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
|
|
| 2. |
- Abarenkov, Kessy, et al.
(author)
-
The curse of the uncultured fungus
- 2022
-
In: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
-
Journal article (peer-reviewed)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
|
|
| 3. |
- Abarenkov, Kessy, et al.
(author)
-
The curse of the uncultured fungus
- 2022
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
-
Journal article (peer-reviewed)abstract
- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
|
|
| 4. |
- Antonelli, Alexandre, 1978, et al.
(author)
-
Amazonia is the primary source of Neotropical biodiversity
- 2018
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 115:23, s. 6034-6039
-
Journal article (peer-reviewed)abstract
- The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate > 1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing > 2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (similar to 1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for > 60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.
|
|
| 5. |
- Antonelli, Alexandre, 1978, et al.
(author)
-
An engine for global plant diversity: Highest evolutionary turnover and emigration in the American tropics
- 2015
-
In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 6:130
-
Journal article (peer-reviewed)abstract
- Understanding the processes that have generated the latitudinal biodiversity gradient and the continental differences in tropical biodiversity remains a major goal of evolutionary biology. Here we estimate the timing and direction of range shifts of extant flowering plants (angiosperms) between tropical and non-tropical zones, and into and out of the major tropical regions of the world. We then calculate rates of speciation and extinction taking into account incomplete taxonomic sampling. We use a recently published fossil calibrated phylogeny and apply novel bioinformatic tools to code species into user-defined polygons. We reconstruct biogeographic history using stochastic character mapping to compute relative numbers of range shifts in proportion to the number of available lineages through time. Our results, based on the analysis of c. 22,600 species and c. 20 million geo-referenced occurrence records, show no significant differences between the speciation and extinction of tropical and non-tropical angiosperms. This suggests that at least in plants, the latitudinal biodiversity gradient primarily derives from other factors than differential rates of diversification. In contrast, the outstanding species richness found today in the American tropics (the Neotropics), as compared to tropical Africa and tropical Asia, is associated with significantly higher speciation and extinction rates. This suggests an exceedingly rapid evolutionary turnover, i.e., Neotropical species being formed and replaced by one another at unparalleled rates. In addition, tropical America stands out from other continents by having "pumped out" more species than it received through most of the last 66 million years. These results imply that the Neotropics have acted as an engine for global plant diversity. © 2015 Antonelli, Zizka, Silvestro, Scharn, Cascales-Miñana and Bacon.
|
|
| 6. |
- Antonelli, Alexandre, 1978, et al.
(author)
-
SUPERSMART: ecology and evolution in the era of big data
- 2014
-
In: PeerJ PrePrints. - : PeerJ. - 2167-9843.
-
Journal article (other academic/artistic)abstract
- Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.
|
|
| 7. |
- Antonelli, Alexandre, 1978, et al.
(author)
-
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
- 2017
-
In: Systematic biology. - : Oxford University Press (OUP). - 1076-836X .- 1063-5157. ; 66:2, s. 152-166
-
Journal article (peer-reviewed)abstract
- Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a "Dated Tree of Life" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].
|
|
| 8. |
- Scharn, Ruud, et al.
(author)
-
Decreased soil moisture due to warming drives community transitions in the tundra
- 2021
-
In: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 16:6
-
Journal article (peer-reviewed)abstract
- Global warming leads to drastic changes in the diversity and structure of Arctic plant communities. Studies of functional diversity within the Arctic tundra biome have improved our understanding of plant responses to warming. However, these studies still show substantial unexplained variation in diversity responses. Complementary to functional diversity, phylogenetic diversity has been useful in climate change studies, but has so far been understudied in the Arctic. Here, we use a 25-year warming experiment to disentangle community responses in Arctic plant phylogenetic diversity across a soil moisture gradient. We found that responses varied over the soil moisture gradient, where meadow communities with intermediate to high soil moisture had a higher magnitude of response. Warming had a negative effect on soil moisture levels in all meadow communities, however meadows with intermediate moisture levels were more sensitive. In these communities, soil moisture loss was associated with earlier snowmelt, resulting in community turnover towards a more heath-like community. This process of "heathification" in the intermediate moisture meadows was driven by the expansion of ericoid and Betula shrubs. In contrast, under a more consistent water supply Salix shrub abundance increased in wet meadows. Due to its lower stature, palatability and decomposability, the increase in heath relative to meadow vegetation can have several large scale effects on the local food web as well as climate. Our study highlights the importance of the hydrological cycle as a driver of vegetation turnover in response to Arctic climate change. The observed patterns in phylogenetic diversity were often driven by contrasting responses of species of the same functional growth form, and could thus provide important complementary information. Thus, phylogenetic diversity is an important tool in disentangling tundra response to environmental change.
|
|
| 9. |
- Scharn, Ruud
(author)
-
Impact of climate warming on Arctic plant diversity: phylogenetic diversity unravels opposing shrub responses in a warming tundra
- 2022
-
Doctoral thesis (other academic/artistic)abstract
- The Arctic biome is at significant risk, with recent observations suggesting that climate change is warming the Arctic nearly four times faster than the global average. Last decade, evidence from experimental warming studies and observations of ambient warming over time shows how increasing air temperature in the Arctic has led to changes to arctic vegetation, and encroachment of trees and shrubs into the tundra. Thus, this amplified Arctic warming is threatening biodiversity, changing vegetation patterns, and thawing permafrost with implications for carbon and nutrient dynamics. These are one of the main concerns of observed plant biodiversity changes (except the loss of biodiversity itself) as they feedback on the global climate through their effects on carbon cycling, albedo, and ecosystem energy balance. Studies of Arctic biodiversity have reported responses in either taxonomic, functional, or phylogenetic diversity, though phylogenetic has so far been understudied in the Arctic. These different measures of quantifying biodiversity will vary in their explanatory value and can have complementary value when looking at the implications of vegetation changes. The overall aim of this thesis is to deepen the knowledge of the effect of ambient and experimental climate warming on taxonomic, functional, and phylogenetic aspects of plant diversity within and between communities. In Latnjajaure (northern Sweden) I used a long-term passive warming experiment using open-top chambers, which include five distinct plant communities. The communities had distinct soil moisture conditions, leading to community-specific responses of the plant growth forms (deciduous shrubs, evergreen shrubs, forbs, and graminoids) and phylogenetic dissimilarity. Moist communities tended to decrease in soil moisture, which drove similarity to dryer, more nutrient-poor communities. Warming significantly affected growth forms, but the direction of the response was not consistent across the communities. Evidence of shrub expansion was found in nearly all communities, with soil moisture determining whether it was driven by deciduous or evergreen shrubs. These changes are expected to affect climate feedback as the dry, evergreen-dominated heath community, has slower carbon cycling. This slowdown in carbon cycling is at least partially due to the evergreen shrubs whose material is harder to decompose than most other arctic vegetation. As the studied communities are common in the region, it is likely that future warming will drive community shifts in the tundra landscape. On a Pan-arctic dataset of warming studies, I explored the effect of scaling abundance weighting as well as the importance of deeper against shallow nodes in the phylogeny on warming response and its interaction with soil moisture and site temperature in the tundra biome. For all metrics, we looked at both plot level (α-diversity), and the difference between plots (β- dissimilarity). We show that β-dissimilarity is more sensitive to warming than α-diversity metrics. Furthermore, we show that sensitivity to abundance and phylogenetic weighting depends on local soil moisture conditions. In conclusion, the combined use of taxonomic, phylogenetic, and functional diversity measures enhances the quality of our assessment of the implications of arctic vegetation response to warming.
|
|
| 10. |
- Scharn, Ruud, et al.
(author)
-
Limited decadal growth of mountain birch saplings has minor impact on surrounding tundra vegetation
- 2022
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 12:6
-
Journal article (peer-reviewed)abstract
- Temperatures over the Arctic region are increasing at three times the rate of the global average. Consequently, Arctic vegetation is changing and trees are encroaching into the tundra. In this study, we examine the establishment and growth of mountain birch (Betula pubescens ssp. tortuosa), which forms the treeline in subarctic Europe, and its impact on community composition across the treeline ecotone nearby Abisko, Sweden. Birch advancement along elevational gradients was studied by comparing data collected in 2016 with data collected 10 and 15years previously. Species identity, cover, and phylogenetic relatedness were used to assess the impact of birch encroachment on community composition. Our results show that birch occurrence above the treeline did not affect plant community composition, probably owing to the observed lack of significant growth due to herbivore browsing, nitrogen limitation, or a reduction in snow cover. Independent of birch performance, the tundra community structure shifted toward a novel community dissimilar from the forest plant community found below the treeline. Taken together, our findings are explained by species-specific responses to climate change, rather than by a linear forest advance. Future treeline advancements are likely more restricted than previously expected
|
|
| 11. |
- Scharn, Ruud, et al.
(author)
-
Vegetation responses to 26 years of warming at Latnjajaure Field Station, northern Sweden
- 2022
-
In: Arctic Science. - 2368-7460. ; 8:3, s. 858-877
-
Journal article (peer-reviewed)abstract
- Climate change is rapidly warming high latitude and high elevation regions influencing plant community composition. Changes in vegetation composition have motivated the coordination of ecological monitoring networks across the Arctic, including the International Tundra Experiment (ITEX). We have established a long-term passive warming experiment using open-top chambers, which includes five distinct plant communities (Dry Heath; Tussock Tundra; and Dry, Mesic, and Wet Meadow). We have measured changes in plant community composition based on relative abundance differences over 26 years. In addition, relative abundance changes in response to fertilization and warming treatments were analysed based on a 7-year Community-Level Interaction Program (CLIP) experiment. The communities had distinct soil moisture conditions, leading to community specific responses of the plant growth forms (deciduous shrubs, evergreen shrubs, forbs and graminoids). Warming significantly affected growth forms, but the direction of the response was not consistent across the communities. Evidence of shrub expansion was found in nearly all communities, with soil moisture determining whether it was driven by deciduous or evergreen shrubs. Graminoids increased in relative abundance in the Dry Meadow due to warming. Growth form responses to warming are likely mediated by edaphic characteristics of the communities and their interactions with climate.
|
|
| 12. |
- Scharn, Ruud, et al.
(author)
-
Vegetation responses to 26 years of warming at Latnjajaure Field Station, northern Sweden
- 2022
-
In: Arctic Science. - Ottawa, ON : Canadian Science Publishing. - 2368-7460. ; 8:3, s. 858-877
-
Journal article (peer-reviewed)abstract
- Climate change is rapidly warming high latitude and high elevation regions influencing plant community composition. Changes in vegetation composition have motivated the coordination of ecological monitoring networks across the Arctic, including the International Tundra Experiment. We have established a long-term passive warming experiment using open-top chambers, which includes five distinct plant communities (Dry Heath; Tussock Tundra; and Dry, Mesic, and Wet Meadow). We measured changes in plant community composition based on relative abundance differences over 26 years. In addition, relative abundance changes in response to fertilization and warming treatments were analyzed based on a seven-year Community-Level Interaction Program experiment. The communities had distinct soil moisture conditions, leading to community-specific responses of the plant growth forms (deciduous shrubs, evergreen shrubs, forbs, and graminoids). Warming significantly affected growth forms, but the direction of the response was not consistent across the communities. Evidence of shrub expansion was found in nearly all communities, with soil moisture determining whether it was driven by deciduous or evergreen shrubs. Graminoids increased in relative abundance in the Dry Meadow due to warming. Growth form responses to warming are likely mediated by edaphic characteristics of the communities and their interactions with climate.
|
|
| 13. |
- Töpel, Mats H., 1973, et al.
(author)
-
SpeciesGeoCoder: Fast categorisation of species occurrences for analyses of biodiversity, biogeography, ecology and evolution.
- 2014
-
In: bioRxiv. - : Cold Spring Harbor Laboratory.
-
Journal article (other academic/artistic)abstract
- Understanding the patterns and processes underlying the uneven distribution of biodiversity across space and time constitutes a major scientific challenge in evolutionary biology. With rapidly accumulating species occurrence data, there is an increasing ne ed for making the process of coding species into operational units for biogeographic and evolutionary analyses faster, automated, transparent and reproducible. Here we present SpeciesGeoCoder, a free software package written in Python and R, that allows fo r easy coding of species into user-defined areas. These areas may be of any size and be purely geographical (i.e., polygons) such as political units, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include al titudinal ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurr ence data. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and NEXUS files that can be directly used in many phylogeny-based applications for ancestral state reconstruction, investiga tions on biome evolution, and diversification rate analyses. Our simulations indicate that even datasets containing hundreds of millions of records can be analysed in relatively short time using a regular desktop computer. We exemplify the use of our progr am through two contrasting examples: i) inferring historical dispersal of birds across the Isthmus of Panama, separating lowland vs. montane species and optimising the results onto a species-level, dated phylogeny; and ii) exploring seasonal variations in the occurrence of 10 GPS-tracked individuals of moose (Alces alces) over one year in northern Sweden. These analyses show that SpeciesGeoCoder allows an easy, flexible and fast categorisation of species distribution data for various analyses in ecology and evolution, with potential use at different spatial, taxonomic and temporal scales.
|
|
| 14. |
- Töpel, Mats H., 1973, et al.
(author)
-
SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.
- 2017
-
In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 66:2, s. 145-151
-
Journal article (peer-reviewed)abstract
- Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity patterns; ecology; evolution; point in polygon; species distribution data.].
|
|
| 15. |
- Zizka, Alexander, et al.
(author)
-
CoordinateCleaner : Standardized cleaning of occurrence records from biological collection databases
- 2019
-
In: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 10:5, s. 744-751
-
Journal article (peer-reviewed)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils.We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic.All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
|
|
| 16. |
- Zizka, Alexander, 1986, et al.
(author)
-
CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
- 2019
-
In: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 10:5, s. 744-751
-
Journal article (peer-reviewed)abstract
- Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r-package to scan datasets of species occurrence records for geo-referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo-referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio-temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open-source and available within the CoordinateCleaner r-package.
|
|
