| 1. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Madagascar's extraordinary biodiversity : Evolution, distribution, and use
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6623, s. 962-
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Journal article (peer-reviewed)abstract
- Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique " living laboratory" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.
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| 2. |
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| 4. |
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| 5. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 6. |
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| 7. |
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| 8. |
- Schmidt, M., et al.
(author)
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Diversity, distribution and preliminary conservation status of the flora of Burkina Faso
- 2017
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In: Phytotaxa. - : Magnolia Press. - 1179-3155 .- 1179-3163. ; 304:1, s. 1-215
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Journal article (peer-reviewed)abstract
- West Africa is a floristically understudied region that is facing severe environmental changes in the 21 st century. Basic distribution data and information on the conservation status for most plant species of the region are scarce, and good information only exists for small areas of interest or for key species. This lack of knowledge seriously hampers urgently needed regional conservation efforts. Here we present comprehensive distribution information and preliminary, automated species conservation assessments for the flora of Burkina Faso, a country in tropical West Africa with a flora and vegetation typical for the savanna belt of the region. We documented and analysed the distribution of 1,568 species or 80% of the flora of Burkina Faso based on an expert curated dataset comprising ca. 150,000 occurrence records from herbarium specimens and vegetation surveys. We used this dataset and environmental niche models to calculate three indicator variables for a preliminary, automated conservation assessment. We classified 350 species (18% of the flora, excluding introduced species) as potentially "Critically Endangered", "Endangered", "Vulnerable" or "Near-Threatened" on the national level. The analyses confirmed species-rich areas in the south-west and south-east of the country, and showed a particular concentration of potentially Endangered species in the south. Furthermore, the proportion of potentially Endangered species differed between plant families, growth forms and habitats. Our results set the base for further plant geographical and ecological studies and are a data-driven baseline for further conservation assessments and large scale conservation strategies of the West African flora.
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| 9. |
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| 10. |
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| 11. |
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| 12. |
- Zizka, Alexander, et al.
(author)
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CoordinateCleaner : Standardized cleaning of occurrence records from biological collection databases
- 2019
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In: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 10:5, s. 744-751
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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.
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| 13. |
- Zizka, Alexander, 1986, et al.
(author)
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CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
- 2019
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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.
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| 14. |
- Zizka, Alexander, 1986, et al.
(author)
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The vascular plant diversity of Burkina Faso (West Africa) - a quantitative analysis and implications for conservation
- 2015
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In: Candollea. - : Society of Conservatoire at Jardin Botaniques de la Ville de Geneve. - 0373-2967. ; 70:1, s. 9-20
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Journal article (peer-reviewed)abstract
- Based on a species inventory and the related distribution dataset, the authors present a quantitative analysis of the vascular plant diversity of Burkina Faso (BFA) and its four phytogeographic zones. We analyzed species richness, higher taxon diversity, life forms, chorological types, introduced species, habitat preferences and the number of rare species. The flora of BFA comprises 1972 non-cultivated vascular plant species in 752 genera and 145 families. Species richness and plant family richness are highest in the South Sudanian zone in the South of the country Fabaceae, Poaceae and Cyperaceae are the most species rich plant families. Only one species (Isoetes jaegeri Pitot) is endemic to the country, whereas the vast majority occurs throughout Africa. The flora is dominated by therophytes and phanerophytes. Our results show a good representation of the West African flora in BFA. The flora and vegetation of the four phytogeographic zones within BFA is determined by the latitudinal climatic gradient of the region. The relative number of phanerophytes and forest species decrease along the gradient, while the relative number of therophytes increase. Based on the specimen record we classified 38% of the plant species as "rare" to BFA. The analyses show that the south-west of BFA is a center of national biodiversity and a potential "hotspot" for conservation. In addition to its high species richness this area harbors the highest number of rare species (409 species, 29%) including the endemic species.
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| 15. |
- Zizka, Alexander, 1986, et al.
(author)
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Traditional plant use in Burkina Faso (West Africa): a national-scale analysis with focus on traditional medicine
- 2015
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In: Journal of Ethnobiology and Ethnomedicine. - : Springer Science and Business Media LLC. - 1746-4269. ; 11:9
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Journal article (peer-reviewed)abstract
- Background: The West African country of Burkina Faso (BFA) is an example for the enduring importance of traditional plant use today. A large proportion of its 17 million inhabitants lives in rural communities and strongly depends on local plant products for their livelihood. However, literature on traditional plant use is still scarce and a comprehensive analysis for the country is still missing. Methods: In this study we combine the information of a recently published plant checklist with information from ethnobotanical literature for a comprehensive, national scale analysis of plant use in Burkina Faso. We quantify the application of plant species in 10 different use categories, evaluate plant use on a plant family level and use the relative importance index to rank all species in the country according to their usefulness. We focus on traditional medicine and quantify the use of plants as remedy against 22 classes of health disorders, evaluate plant use in traditional medicine on the level of plant families and rank all species used in traditional medicine according to their respective usefulness. Results: A total of 1033 species (50%) in Burkina Faso had a documented use. Traditional medicine, human nutrition and animal fodder were the most important use categories. The 12 most common plant families in BFA differed considerably in their usefulness and application. Fabaceae, Poaceae and Malvaceae were the plant families with the most used species. In this study Khaya senegalensis, Adansonia digitata and Diospyros mespiliformis were ranked the top useful plants in BFA. Infections/Infestations, digestive system disorders and genitourinary disorders are the health problems most commonly addressed with medicinal plants. Fabaceae, Poaceae, Asteraceae, Apocynaceae, Malvaceae and Rubiaceae were the most important plant families in traditional medicine. Tamarindus indica, Vitellaria paradoxa and Adansonia digitata were ranked the most important medicinal plants. Conclusions: The national-scale analysis revealed systematic patterns of traditional plant use throughout BFA. These results are of interest for applied research, as a detailed knowledge of traditional plant use can a) help to communicate conservation needs and b) facilitate future research on drug screening.
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| 16. |
- Andermann, Tobias, et al.
(author)
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SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
- 2018
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In: Peerj. - : PeerJ. - 2167-8359. ; 6
-
Journal article (peer-reviewed)abstract
- Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproducible way. To tackle these challenges we introduce the Sequence Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple sequence alignments for downstream phylogenetic and phylogeographic analyses. SECAPR is user-friendly and we provide an exhaustive empirical data tutorial intended for users with no prior experience with analyzing MPS output. SECAPR is particularly useful for the processing of sequence capture (synonyms: target or hybrid enrichment) datasets for non-model organisms, as we demonstrate using an empirical sequence capture dataset of the palm genus Geonoma (Arecaceae). Various quality control and plotting functions help the user to decide on the most suitable settings for even challenging datasets. SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and reproducible processing of MPS data for many samples in parallel.
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| 17. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Amazonia is the primary source of Neotropical biodiversity
- 2018
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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.
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| 18. |
- Antonelli, Alexandre, 1978, et al.
(author)
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An engine for global plant diversity: Highest evolutionary turnover and emigration in the American tropics
- 2015
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In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 6:130
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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.
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| 19. |
- Antonelli, Alexandre, 1978, et al.
(author)
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Conceptual and empirical advances in Neotropical biodiversity research
- 2018
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In: PeerJ. - : PeerJ. - 2167-8359. ; 2018:10
-
Journal article (peer-reviewed)abstract
- The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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| 20. |
- Aronsson, Heléne, 1994, et al.
(author)
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Expert-based range maps cannot be replicated using data-driven methods but macroecological conclusions arising from them can
- 2024
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In: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
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Journal article (peer-reviewed)abstract
- AimAnswering many fundamental and applied scientific questions relies on accurate geographic range maps for species, such as those compiled by experts working with the International Union for Conservation of Nature (IUCN). However, these maps are resource demanding to produce and only available for a limited number of organisms. Here, we test to what extent standardized, data-driven methods based on publicly available occurrences can reproduce expert-based IUCN range maps and the macroecological conclusions drawn from them.LocationGlobal.Time PeriodPresent.TaxaBirds.Materials and MethodsWe estimated the geographic ranges for 7385 non-marine bird species which either were non-migratory or had spatially connected breeding and wintering ranges from publicly available, georeferenced point occurrences. We then quantified the spatial overlap between these range estimates and the IUCN expert-derived range estimates. Finally, we compared global species richness patterns and the environmental correlates that emerge from both approaches.ResultsWe find that range estimates based on point occurrence records overlap on average 52% with expert range estimates for the same species. The global species richness patterns estimated under both approaches are overall similar but show local and regional differences, for example, in the tropical Andes of northern South America and the Central Arc region of Africa. The estimated global drivers of richness are similar.Main ConclusionsExpert-derived estimates of species distributions are not reproducible by data-driven approaches relying on currently available public records, even for well-documented taxa such as birds. However, these discrepancies do not substantially change our macroecological understanding of global drivers of bird diversity.
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| 21. |
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| 22. |
- Calvente, Alice, et al.
(author)
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Spiny but photogenic : amateur sightings complement herbarium specimens to reveal the bioregions of cacti
- 2023
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In: American Journal of Botany. - : John Wiley & Sons. - 0002-9122 .- 1537-2197. ; 110:10
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Journal article (peer-reviewed)abstract
- Premise: Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. We tested global biogeographic boundaries for Neotropical Cactaceae using specimen-based occurrences, coupled with data from visual observations, as a means to tackle the known collection biases in the family.Methods: Species richness and record density were assessed for preserved specimens and human observations, and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions, based on data from 261,272 point records cleaned through automated and manual steps.Results: We found that areas in Mexico and southwestern USA, in eastern Brazil, and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cactus bioregions, among which the most species-rich are northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, and Mexico/Baja California.Conclusions: The bioregionalization proposed shows biogeographic boundaries specific to cacti and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert-derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen-science records, can complement traditional specimen-based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.
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| 23. |
- Edler, Daniel, et al.
(author)
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Infomap Bioregions : Interactive Mapping of Biogeographical Regions from Species Distributions
- 2017
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In: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 66:2, s. 197-204
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Journal article (peer-reviewed)abstract
- Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology, and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here, we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional, or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles, or in table format. We validate the tool by processing large data sets of publicly available species distribution data of the world's amphibians using species ranges, and mammals using point occurrences. We then calculate the fit between the inferred bioregions and WWF ecoregions. As examples of applications, researchers can reconstruct ancestral ranges in historical biogeography or identify indicator species for targeted conservation.
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| 24. |
- Guedes, Thaís, et al.
(author)
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Patterns, biases and prospects in the distribution and diversity of Neotropical snakes
- 2018
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In: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 27:1, s. 14-21
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Journal article (peer-reviewed)abstract
- Motivation: We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases. Main types of variables contained: We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset. Spatial location and grain: Neotropics, Behrmann projection equivalent to 1 degrees x 1 degrees. Results: The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well-sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed. Main conclusions: The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high-diversity areas and sampling efforts be directed towards Amazonia and poorly known species.
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| 25. |
- Maldonado, C., et al.
(author)
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Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?
- 2015
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In: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 24:8, s. 973-984
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Journal article (peer-reviewed)abstract
- AimMassive digitalization of natural history collections is now leading to a steep accumulation of publicly available species distribution data. However, taxonomic errors and geographical uncertainty of species occurrence records are now acknowledged by the scientific community - putting into question to what extent such data can be used to unveil correct patterns of biodiversity and distribution. We explore this question through quantitative and qualitative analyses of uncleaned versus manually verified datasets of species distribution records across different spatial scales. MethodsAs test case we used the plant tribe Cinchoneae (Rubiaceae). We compiled four datasets of species occurrences: one created manually and verified through classical taxonomic work, and the rest derived from GBIF under different cleaning and filling schemes. We used new bioinformatic tools to code species into grids, ecoregions, and biomes following WWF's classification. We analysed species richness and altitudinal ranges of the species. ResultsAltitudinal ranges for species and genera were correctly inferred even without manual data cleaning and filling. However, erroneous records affected spatial patterns of species richness. They led to an overestimation of species richness in certain areas outside the centres of diversity in the clade. The location of many of these areas comprised the geographical midpoint of countries and political subdivisions, assigned long after the specimens had been collected. Main conclusionOpen databases and integrative bioinformatic tools allow a rapid approximation of large-scale patterns of biodiversity across space and altitudinal ranges. We found that geographic inaccuracy affects diversity patterns more than taxonomic uncertainties, often leading to false positives, i.e. overestimating species richness in relatively species poor regions. Public databases for species distribution are valuable and should be more explored, but under scrutiny and validation by taxonomic experts. We suggest that database managers implement easy ways of community feedback on data quality.
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| 26. |
- Mikryukov, Vladimir, et al.
(author)
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Connecting the multiple dimensions of global soil fungal diversity
- 2023
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In: Science advances. - 2375-2548. ; 9:48
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Journal article (peer-reviewed)abstract
- How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.
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| 27. |
- Ritter, Camila, et al.
(author)
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High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.
- 2018
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In: PeerJ. - : PeerJ. - 2167-8359. ; 6
-
Journal article (peer-reviewed)abstract
- Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).In spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world's largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.
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| 28. |
- Ritter, Camila, et al.
(author)
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Locality or habitat? Exploring predictors of biodiversity in Amazonia
- 2019
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In: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 42:2, s. 321-333
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Journal article (peer-reviewed)abstract
- © 2018 Nordic Society Oikos. Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above-ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large-scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro-organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced. Ecography
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| 29. |
- Ritter, Camila, et al.
(author)
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The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia
- 2019
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Journal article (peer-reviewed)abstract
- © 2019, The Author(s). Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.
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| 30. |
- Rydén, Oskar, et al.
(author)
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Linking democracy and biodiversity conservation: Empirical evidence and research gaps
- 2020
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In: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 49, s. 419-433
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Journal article (peer-reviewed)abstract
- Increasing human pressure threatens plant and animal species with extinction worldwide. National political institutions constitute an important arena for biodiversity conservation. Yet, the relationship between how democratic these national institutions are and a country’s efforts towards and track-record for biodiversity conservation remains poorly understood. In this review, we outline the theoretical links between democracy and biodiversity conservation and review the empirical literature testing them. While more studies reported a positive than a negative relation between democracy and biodiversity conservation (15 vs. 11), the most common result was a mixed relationship (28), often conditioned on economic factors. The use of different proxies to measure biodiversity, including deforestation, protected areas, threatened species, and fishery statistics emerged as a primary obstacle for synthesis. We suggest overcoming this caveat together with a consistent definition of democratic institutions and a standardized statistical framework as research priorities to improve policies against the global biodiversity loss. © 2019, The Author(s).
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| 31. |
- Silvestro, Daniele, et al.
(author)
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Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors
- 2019
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In: Systematic biology. - : Oxford University Press (OUP). - 1076-836X .- 1063-5157. ; 68:1, s. 78-92
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Journal article (peer-reviewed)abstract
- New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5-10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small-weighing 0.4 kg-and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
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| 32. |
- Silvestro, Daniele, et al.
(author)
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Fossil biogeography: A new model to infer dispersal, extinction and sampling from palaeontological data
- 2016
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In: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 371:1691
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Journal article (peer-reviewed)abstract
- © 2016 The Author(s) Published by the Royal Society. All rights reserved.Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters.We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene.We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
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| 33. |
- Tedersoo, Leho, et al.
(author)
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Global patterns in endemicity and vulnerability of soil fungi.
- 2022
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In: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
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Journal article (peer-reviewed)abstract
- Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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| 34. |
- Töpel, Mats H., 1973, et al.
(author)
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SpeciesGeoCoder: Fast categorisation of species occurrences for analyses of biodiversity, biogeography, ecology and evolution.
- 2014
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In: bioRxiv. - : Cold Spring Harbor Laboratory.
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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.
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| 35. |
- Töpel, Mats H., 1973, et al.
(author)
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SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.
- 2017
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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.].
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| 36. |
- Zizka, Alexander, 1986
(author)
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Big data suggest migration and bioregion connectivity as crucial for the evolution of Neotropical biodiversity
- 2019
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In: Frontiers of Biogeography. - 1948-6596. ; 11:2
-
Journal article (peer-reviewed)abstract
- © the authors. Tropical America (the Neotropics) is the most biodiverse realm on Earth and might harbour more species than tropical Asia and Africa combined. The evolutionary history generating this outstanding diversity remains poorly understood partly because data on the geographic distribution of species are scarce. Collections from museums and herbaria can overcome this gap, but uncertain data quality hampers their use, especially in historical biogeography. Here, I highlight the results from recent studies quantifying diversification and bioregion connectivity in the Neotropics using large-scale species occurrence data, and argue that (i) recently developed software to analyse large-scale data provides a methodological route forward for biogeography, and (ii) biotic connectivity within and among bioregions is a common, but underappreciated, process in the evolution of Neotropical diversity.
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| 37. |
- Zizka, Alexander, et al.
(author)
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Exploring the Impact of Political Regimes on Biodiversity
- 2020
-
In: SSRN Electronic Journal. - Göteborg : Göteborgs universitet. - 1556-5068.
-
Other publication (other academic/artistic)abstract
- National governments are the main actors responsible for mapping and protecting their biodiversity, but countries differ in their capacity, willingness, and effectiveness to do so. We quantify the global biodiversity managed by different regime types and developed a tool to explore the links between level of democracy and other key socio-economic variables with the number of natural history specimens registered within country boundaries. Using this tool, distinct and previously unknown patterns emerge around the world, that urge for increased collaboration between the natural and social sciences to further explore these patterns and their underlying processes.
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| 38. |
- Zizka, Alexander, 1986, et al.
(author)
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Finding needles in the haystack: Where to look for rare species in the American tropics
- 2018
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In: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 41:2, s. 321-330
-
Journal article (peer-reviewed)abstract
- © 2016 Nordic Society Oikos. Tropical America (the Neotropics) harbours more plant species than any other region on Earth. The contribution of rare species to this diversity has been recently recognised, but their spatial distribution remains poorly understood. Here, we use all collection records of angiosperms from the Global Biodiversity Information Facility to delineate Neotropical bioregions, and to identify putatively rare species within the Neotropics and the Amazonian rainforest. We analyse the spatial distribution of these species and validate the results on a largely independent dataset based on vegetation plots from the Amazon Tree Diversity Network. We find that rare species are homogeneously distributed through most parts of the lowland Neotropics and Amazonia, but more concentrated in highlands. The second collection of any rare species is most often found in the close vicinity of the first, but in 20% of cases they are more than 580 km apart. We also find cross-taxonomic patterns of disjunct distributions within the Andes, the Atlantic forest in eastern Brazil, and between Amazonia and the Atlantic forest, but no clear disjunction patterns within lowland areas. These results suggest that a considerable proportion of rare plant species have surprisingly large distribution ranges, and that collections of rare species across most of the lowland Neotropics, and in particular in Amazonia, show no clear directionality. The second record of many rare species may be found virtually anywhere, urging the need for intensifying and broadening biological sampling.
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| 39. |
- Zizka, Alexander, 1986, et al.
(author)
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How to tell a shrub from a tree: A life-history perspective from a South African savanna
- 2014
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In: Austral Ecology. - : Wiley. - 1442-9985 .- 1442-9993. ; 39:7, s. 767-778
-
Journal article (peer-reviewed)abstract
- The ecological differences between shrubs' and trees' are surprisingly poorly understood and clear ecological definitions of these two constructs do not exist. It is not clear whether a shrub is simply a small tree or whether shrubs represent a distinct life-history strategy. This question is of special interest in African savannas, where shrubs and trees often co-dominate, but are often treated uniformly as woody plants' even though the tree to shrub ratio is an important determinant of ecosystem functioning. In this study we use data from a long-term fire experiment, together with a trait-based approach to test (i) if woody species usually classified as shrubs or trees in African savanna differ in key traits related to disturbance and resource use; and (ii) if these differences justify the interpretation of the two growth forms as distinct life-history strategies. We measured for 22 of the most common woody plant species of a South African savanna 27 plant traits related to plant architecture, life-history, leaf characteristics, photosynthesis and resprouting capacity. Furthermore we evaluated their performance during a long-term fire experiment. We found that woody plants authors call (i) shrubs; (ii) shrubs sometimes small trees; and (3) trees responded differently to long-term fire treatments. We additionally found significant differences in architecture, diameter-height-allometry, foliage density, resprouting vigour after fire, minimum fruiting height and foliar C-13 between these three woody plant types. We interpret these findings as evidence for at least two different life-history-strategies: an avoidance/adaptation strategy for shrubs (early reproduction+adaptation to minor disturbance) and an escape strategy for trees (promoted investment in height growth+delayed reproduction).
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| 40. |
- Zizka, Alexander, 1986, et al.
(author)
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Transitions between biomes are common and directional in Bombacoideae (Malvaceae)
- 2020
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In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 47:6, s. 1310-1321
-
Journal article (peer-reviewed)abstract
- Aim To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location The tropics. Time period The Cenozoic. Major taxa studied The plant subfamily Bombacoideae (Malvaceae). Methods We inferred ancestral biomes based on a fossil-dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal-extinction-cladogenesis model. We then estimated diversification rates using state-specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis.
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