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| Aliabadian, M.; Nijman, V.; Mahmoudi, A.; Naderi, M.; Vonk, R.; Vences, M.. |
| In the context of DNA Barcoding, sequences of standard marker genes for thousands and potentially millions of individuals and species are becoming available, requiring ever more efficient bioinformatic environments and software algorithms for analysis. We here present ExcaliBAR (Extraction, Calculation, Barcoding), a user-friendly software utility to facilitate one important initial step in DNA barcoding analyses, namely the determination of the barcoding gap between pairwise genetic distances among and within species, based on original distance matrices computed by MEGA software. In addition, the software is able to rename sequences downloaded via the standard user interfaces of public databases such as GenBank, without the need of developing and applying... |
| Tipo: Article / Letter to the editor |
Palavras-chave: Bioinformatics DNA Barcoding pairwise genetic distance sequence renaming 35.73 42; 20 54.50. |
| Ano: 2014 |
URL: http://www.repository.naturalis.nl/record/474212 |
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| Aliabadian, M.; Roselaar, C.S.; Sluys, R.; Nijman, V.. |
| In the study of diversity patterns, the Mid-domain effect (MDE), which explains gradients in diversity solely on the basis of geometric constraints, has emerged as a null-model against which other hypotheses can be tested. The effectiveness, measured by its predictive power, of these MDE models appears to depend on the size of the study area and the range-sizes of the taxa considered. Here we test the predictive power of MDE on the species richness patterns of birds and assess its effectiveness for a variety of species range sizes. We digitised distribution maps of 889 species of songbird endemic to the Palearctic, and analysed the emergent biogeographic patterns with WORLDMAP software. MDE had a predictive power of 20% when all songbirds were included.... |
| Tipo: Article / Letter to the editor |
Palavras-chave: Aves; Passeriformes; Palearctic; Mid-domain effect; Species richness; Geographic range size; 42.83. |
| Ano: 2007 |
URL: http://www.repository.naturalis.nl/record/256132 |
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| Aliabadian, M.; Sluys, R.; Roselaar, C.S.; Nijman, V.. |
| Explanation of the spatial distribution patterns in species richness, and especially those of small-ranged species (endemics), bears relevance for studies on evolution and speciation, as well as for conservation management. We test a geometric constraint model, the mid-domain effect (MDE), as a possible explanation for spatial patterns of species richness in Palearctic songbirds (Passeriformes), with an emphasis on the patterns of small-ranged species. We calculated species richness based on digitised distribution maps of phylogenetic species of songbirds endemic to the Palearctic region. Data were plotted and analyzed over a one degree longitude equal area map of the Palearctic Region, with a grid cell area of 4062 km². The emergent biogeographic patterns... |
| Tipo: Article / Letter to the editor |
Palavras-chave: Aves endemism hotspot analysis mid-domain effect Palearctic; Songbirds 42.83. |
| Ano: 2008 |
URL: http://www.repository.naturalis.nl/record/280478 |
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