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- Torres Jimenez, Maria Fernanda, et al.
(författare)
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Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella
- 2021
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Ingår i: Systematic Botany. - : American Society of Plant Taxonomists. - 0363-6445. ; 46:3, s. 863-874
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Tidskriftsartikel (refereegranskat)abstract
- The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge, limiting our understanding of its systematics, morphology, and biogeography. Several aspects make the tribe an ideal system to study plant evolution and diversity: it is well-represented in the fossil record as a prolific pollen producer, its continental diversity contradicts common biodiversity patterns of lower species richness in Africa in comparison to South America, and it contains one of the most abundant Amazonian tree species, Mauritia flexuosa. Here, we investigated the systematics of the tribe by sampling 122 individuals representing 42 species (82% of the tribe), using target sequence capture. We recovered nearly 10,000 single nucleotide polymorphisms from nuclear and plastid DNA across 146 target sequences to separately infer a phylogenomic tree. Our results strongly support inter-generic and inter-specific relationships, where a majority of nodes were resolved with over 90% bootstrap support. We also identify strong phylogenetic support for the recognition of a new species from central and south Amazonia, Mauritiella disticha. The distichous phyllotaxy is diagnostic of the species within the genus. Rare and currently only known from the middle-lower Madeira River basin in the state of Amazonas, Brazil, M. disticha is restricted to open vegetation and forest edges growing in white sand habitats with saturated or well-drained soils. Our preliminary red list assessment suggests its threatened status to be vulnerable (VU). We use our phylogenomic inference to define and contextualize systematic relationships in the tribe, and present a formal species description.
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| 2. |
- Ryska, P., et al.
(författare)
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Variability of Normal Pressure Hydrocephalus Imaging Biomarkers with Respect to Section Plane Angulation : How Wrong a Radiologist Can Be?
- 2021
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Ingår i: American Journal of Neuroradiology. - : American Society of Neuroradiology. - 0195-6108 .- 1936-959X. ; 42:7, s. 1201-1207
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND PURPOSE: Systematic analysis of angulation-related variability of idiopathic normal pressure hydrocephalus imaging biomarkers has not been published yet. Our aim was to evaluate the variability of these radiologic biomarkers with respect to imaging plane angulation.MATERIALS AND METHODS: Eighty subjects (35 with clinically confirmed idiopathic normal pressure hydrocephalus and 45 age- and sex-matched healthy controls) were prospectively enrolled in a 3T brain MR imaging study. Two independent readers assessed 12 radiologic idiopathic normal pressure hydrocephalus biomarkers on sections aligned parallel or perpendicular to the bicallosal, bicommissural, hypophysis-fastigium, and brain stem vertical lines, respectively.RESULTS: Disproportionately enlarged subarachnoid space hydrocephalus, simplified callosal angle, frontal horn diameter, z-Evans Index, and cella media vertical width did not show significant systematic differences in any of 6 section plane combinations studied. The remaining 7 biomarkers (including the Evans Index and callosal angle) showed significant differences in up to 4 of 6 mutually compared section plane combinations. The values obtained from sections aligned with the brain stem vertical line (parallel to the posterior brain stem margin) showed the most deviating results from other section angulations.CONCLUSIONS: Seven of 12 idiopathic normal pressure hydrocephalus biomarkers including the frequently used Evans Index and callosal angle showed statistically significant deviations when measured on sections whose angulations differed or did not comply with the proper section definition published in the original literature. Strict adherence to the methodology of idiopathic normal pressure hydrocephalus biomarker assessment is, therefore, essential to avoid an incorrect diagnosis. Increased radiologic and clinical attention should be paid to the biomarkers showing low angulation-related variability yet high specificity for idiopathic normal pressure hydrocephalus-related morphologic changes such as the z-Evans Index, frontal horn diameter, or disproportionately enlarged subarachnoid space hydrocephalus.
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| 3. |
- Schneider, J. V., et al.
(författare)
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Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+taxa
- 2021
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Ingår i: Taxon. - : Wiley. - 0040-0262 .- 1996-8175. ; 70:1, s. 48-71
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Tidskriftsartikel (refereegranskat)abstract
- Targeted capture of nuclear genes increasingly contributes to unravelling phylogenetic relationships that hitherto remained unresolved because of limitations of traditional Sanger sequencing. In particular, the study of tropical plant families has been compromised because they often rely on highly degraded DNA obtained from herbarium specimens. One such example is the pantropical Ochnaceae, which comprises 33 genera and approximately 550 species, occurring mostly in savannas and moist tropical forests. Here, we developed a set of baits covering about 660,000 bp from 275 nuclear genes used for the targeted enrichment based on all but one genus and more than 250 species. Using this novel dataset, we resolved the phylogenetic backbone of Ochnaceae, including that of Ochninae, and we established new relationships. Most importantly, our findings highlight that the neotropical and palaeotropical taxa of Sauvagesia form independent clades, requiring the re-erection of formerly separate genera. Ouratea and Ochna (both Ochninae), by far the most species-rich genera and represented by 120 and 41 species, respectively, came out as monophyletic. In contrast, the third-most species-rich genus, Campylospermum, is polyphyletic in two distinct clades. Ouratea, the only neotropical genus of Ochninae, was sister to the five palaeotropical genera of this subtribe. The bait kit developed in this study proved to be particularly useful for unravelling relationships within Ochninae, which includes about two-thirds of the species diversity in the family.
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| 4. |
- Zizka, A., et al.
(författare)
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Automated conservation assessment of the orchid family with deep learning
- 2021
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Ingår i: Conservation Biology. - : Wiley. - 0888-8892 .- 1523-1739. ; 35:3, s. 897-908
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Tidskriftsartikel (refereegranskat)abstract
- International Union for Conservation of Nature (IUCN) Red List assessments are essential for prioritizing conservation needs but are resource intensive and therefore available only for a fraction of global species richness. Automated conservation assessments based on digitally available geographic occurrence records can be a rapid alternative, but it is unclear how reliable these assessments are. We conducted automated conservation assessments for 13,910 species (47.3% of the known species in the family) of the diverse and globally distributed orchid family (Orchidaceae), for which most species (13,049) were previously unassessed by IUCN. We used a novel method based on a deep neural network (IUC-NN). We identified 4,342 orchid species (31.2% of the evaluated species) as possibly threatened with extinction (equivalent to IUCN categories critically endangered [CR], endangered [EN], or vulnerable [VU]) and Madagascar, East Africa, Southeast Asia, and several oceanic islands as priority areas for orchid conservation. Orchidaceae provided a model with which to test the sensitivity of automated assessment methods to problems with data availability, data quality, and geographic sampling bias. The IUC-NN identified possibly threatened species with an accuracy of 84.3%, with significantly lower geographic evaluation bias relative to the IUCN Red List and was robust even when data availability was low and there were geographic errors in the input data. Overall, our results demonstrate that automated assessments have an important role to play in identifying species at the greatest risk of extinction.
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| 5. |
- Zizka, A., et al.
(författare)
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Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space
- 2021
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:11, s. 2715-2726
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Tidskriftsartikel (refereegranskat)abstract
- Aim Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (), an open-source software to explore the relationship between the availability of species occurrence records and the political framework in countries worldwide and through time. Location Global. Taxon Any. Methods Bio-Dem accesses the number of occurrence records available from countries worldwide from the Global Biodiversity Information Facility () and socio-political information from these countries from the Varieties of Democracy database () as well as information on colonial history from the Issue Correlates of War Project. Results Bio-Dem is available as a free graphical user interface web application at . Through three interactive graphs, Bio-Dem enables users to explore the relationship between species occurrence records and countries' regime type, freedom of movement, freedom of association, gross domestic product, education length, political corruption, armed conflict and colonial history. We describe possible links of these specific political indicators with the collection and mobilization of biodiversity data. Illustrative examples and video tutorials explaining the use of Bio-Dem are available at . Main conclusions Bio-Dem provides a user-friendly way to explore the link between socio-political variables and the availability of species occurrence records in user-selected taxa and geographic regions, and to generate hypotheses on their connection. We envision Bio-Dem as a useful tool for teachers communicating the caveats of available biodiversity data, for biodiversity scientists exploring potential spatial and temporal bias in their data, and for social scientists exploring the impact of political systems on scientific data collection and biodiversity conservation.
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| 6. |
- Zizka, A., et al.
(författare)
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sampbias, a method for quantifying geographic sampling biases in species distribution data
- 2021
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Ingår i: Ecography. - : Wiley. - 0906-7590 .- 1600-0587. ; 44:1, s. 25-32
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Tidskriftsartikel (refereegranskat)abstract
- Geo-referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility are ubiquitous but may differ in strength among taxonomic groups and data sets. Although several factors have been described to influence human access (such as presence of roads, rivers, airports and cities), quantifying their specific and combined effects on recorded occurrence data remains challenging. Here we present sampbias, an algorithm and software for quantifying the effect of accessibility biases in species occurrence data sets. sampbias uses a Bayesian approach to estimate how sampling rates vary as a function of proximity to one or multiple bias factors. The results are comparable among bias factors and data sets. We demonstrate the use of sampbias on a data set of mammal occurrences from the island of Borneo, showing a high biasing effect of cities and a moderate effect of roads and airports. sampbias is implemented as a well-documented, open-access and user-friendly R package that we hope will become a standard tool for anyone working with species occurrences in ecology, evolution, conservation and related fields. © 2020 The Authors. Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos
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