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  • 1
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    ExcaliBAR: a simple and fast software utility to calculate intra- and interspecific distances from DNA barcodes (2014)
    In:  Contributions to Zoology vol. 83 no. 1, pp. 79-83
    Details
    Publication Date: 2024-01-12
    Description: 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 specific scripts for this purpose.
    Keywords: bioinformatics ; DNA Barcoding ; pairwise genetic distance ; sequence renaming
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
    Format: application/pdf
    Format: application/x-ms-dos-executable
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  • 2
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    Low predictive power of mid-domain effect to explain geographic species richness patterns in Palearctic songbirds (2007)
    In:  Contributions to Zoology vol. 76 no. 3, pp. 197-204
    Details
    Publication Date: 2024-01-12
    Description: 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. Major hotspots were located south of the area where MDE predicted the highest species-richness, and some of the observed coldspots were in the centre of the Palearctic, contradicting the predictions of the MDE. MDE had little explanatory power (3-19%) for all but the largest range sizes, whereas MDE performed equal or better for the large-ranged species (20-34%) compared to the overall model. Overall MDE did not accurate explain species-richness patterns in Palearctic songbirds. Subsets of larger-range species did not always have a larger predictive power than smaller-range species or the overall model. Despite their low predictive power, MDE models can have a role to play in explaining biogeographic patterns but other variables need to be included in the model as well.
    Keywords: Aves ; Passeriformes ; Palearctic ; mid-domain effect ; species richness ; geographic range size
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 3
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    Avian hybrids: incidence and geographic distribution of hybridisation in birds (2007)
    Oxford University Press
    In:  Handbook of Avian Hybrids of the World vol. 76, 1, pp. 59-61
    Details
    Publication Date: 2024-01-12
    Keywords: book review ; geographic distribution ; hybridisation ; birds
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/review
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  • 4
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    Species diversity and endemism: testing the mid-domain effect on species richness patterns of songbirds in the Palearctic Region (2008)
    In:  Contributions to Zoology vol. 77 no. 2, pp. 99-108
    Details
    Publication Date: 2024-01-12
    Description: 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 km\xc2\xb2. The emergent biogeographic patterns were analysed with WORLDMAP software. Comparison of the observed richness pattern among 2401 phylogenetic taxa of songbirds in the Palearctic Region with the predictions of a fully stochastic bi-dimensional MDE model revealed that this model has limited empirical support for overall species richness of Palearctic songbirds. Major hotspots were located south of the area where MDE predicted the highest species- richness, while some of the observed coldspots were in the centre of the Palearctic Region. Although small-ranged species are often found in areas with the highest species richness, MDE models have a very restricted explanatory power for the observed species-richness pattern in small-ranged species. Regions with a high number of small-ranged species (endemism hotspots) may contain a unique set of environmental conditions, unrelated to the shape or size of the domain, allowing a multitude of species to co-exist.
    Keywords: Aves ; endemism ; hotspot analysis ; mid-domain effect ; Palearctic ; songbirds
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 5
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    Effect of introduced species and habitat alteration on the occurrence and distribution of euryhaline fishes in fresh- and brackish-water habitats on Aruba, Bonaire and Cura\xc3\xa7ao (South Caribbean) (2008)
    In:  Contributions to Zoology vol. 77 no. 1, pp. 45-52
    Details
    Publication Date: 2024-01-12
    Description: We conducted an ichthyological survey during the dry season of 2006 on the semi-arid islands of Aruba, Bonaire and Cura\xc3\xa7ao to provide information on species composition, richness and distribution in natural and non-natural aquatic habitats. The dry season species assemblages (N = 9 species) comprised less species than the wet seasons, and these data refine our knowledge of the indigenous fish fauna and its refuge localities during phases of drought and ensuing high salinity. A hierarchical cluster analysis reveals that the three islands have different species compositions with Cura\xc3\xa7ao being the most diverse, probably due to its having the most habitats and freshwaters present throughout the year. Species richness was unrelated to salinity and species diversity was highest in canalised streams. In the dry season fewer amphidromous species are present than in the wet season. We found no significant effect of human-induced changes on the presence or absence of fish species in the Netherlands Antilles. The presence of exotic species (including Xiphophorus helleri on Aruba, a first record for this island, and Oreochromis mossambicus and Poecilia reticulata occurring on all three islands) did not have a clear effect on the presence of indigenous species, nor did human alteration of the habitats have an influence on the occurrence of fish species.
    Keywords: fish assemblages ; semi-arid islands ; intermittent rivers ; aquatic refugia ; ecological integrity
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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