Search bioRxiv⌕ Search

Biology subjects

Kandziora, M.

Publications and source records attributed to Kandziora, M..

4 recordsLinked to original sources

Different resource partitioning explains plant species richness patterns in tropical alpine ecosystems

Species co-existence based on resource partitioning modulates biodiversity patterns across latitudes and altitudes. Resource partitioning can occur via specialisation or separation in the geographic range or niche. Here, we compare two tropical alpine ecosystems with similar climates to test for geographic range and climatic niche partitioning strategies in explaining species richness difference. We compare the species-rich tropical alpine ecosystem in the South American Andes with the more species-poor one in the eastern African mountains. We combine phylogenomic data for three locally diversified plant lineages in each region with occurrence records and estimate climatic niche and geographic range metrics (size and overlap). We found that the Andean species have overall larger niches than the African species, thus smaller niches indicating specialisation is not the explanation for the higher species richness in the Andes. Instead, for species with overlapping geographic ranges, we found that the Andean species tend to show less niche overlap than the African species, indicating more effective niche separation. Taken together, we propose that different degrees of niche separation in geographically overlapping species, and hence, a different pattern of resource partitioning, explain the differences in species richness between the two tropical alpine ecosystems.

ecology↗

PhylUp: phylogenetic alignment building with custom taxon sampling

In recent years it has become easier to reconstruct large-scale phylogenies with more or less automated workflows. However, they do not permit to adapt the taxon sampling strategy for the clade of interest. While most tools permit a single representative per taxon, PhylUp - the workflow presented here - enables to use different sampling strategies for different taxonomic ranks, as often needed for molecular dating analyses or for a large outgroup sampling. While PhylUp focuses on user-defined sampling strategies, it also facilitates the updating of alignments with new sequences from local and online sequence databases and their incorporation into existing alignments. To start a PhylUp run at least one sequence per locus has to be provided, PhylUp then adds new sequences to the existing one by internally using BLAST to find similar sequences and filters them according to user settings. Taxonomic sampling is increased compared to available tools and the custom taxonomic sampling allows to use automated workflows for new research fields. The workflow is presented in detail and I demonstrate the usability.

bioinformatics↗

Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life

O_LIPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. C_LIO_LIPhyscraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. C_LIO_LIPhyscraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). C_LIO_LIThe Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs. C_LI

bioinformatics↗

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

AO_SCPCAPBSTRACTC_SCPCAPThe coincidence of long distance dispersal and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a \"stepping stone\" between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. These results highlight the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.\n\nThis article has been peer-reviewed and recommended by: Peer Community in Evolutionary Biology (DOI: 10.24072/pci.evolbiol.100065)

evolutionary biology↗