Mikula, O. | Search bioRxiv

bioRxiv2018

Genetic hubs: a phylogeographer’s widget for pinpointing of ancestral populations

Statistical phylogeography benefits from the development of increasingly realistic models of spatially structured genetic variation. Their fitting, however, is computationally demanding and requires population and/or genomic sampling that is not available for many species of interest. Genetic hubs is a method that can be used for exploratory analyses of various kinds of genetic data, including those as typical in mitochondrial phylogeography, i.e. many small samples of single locus genotypes scattered throughout the species distributional range. Genetic hubs allows to quantify and visualize gradients of genetic variation with the aim to pinpoint possible origin of expansion. It estimates local genetic variability as an accessibility of all genetic variation from the site in question and it allows to take dissimilarity of genotypes into account. The method represents fast and versatile tool that can be used whenever history of range expansion is assumed to shape the observed distribution of genetic variation and it is useful especially for preliminary analyses whose purpose is to provide sound basis for formulation of testable hypotheses and design of follow-up studies.

evolutionary biology↗

bioRxiv2018

Cutting tree branches to pick OTUs: a novel method of provisional species delimitation

Delimitation of species is crucial in all studies of biodiversity, its geographic patterns and evolutionary dynamics as well as in the corresponding conservation applications. In practice, operational taxonomic units (OTUs) are often used as provisional surrogates of the species, whose evidence-based and robust delimitation requires too extensive data and complex analyses. The novel method for this provisional species delimitation is suggested, which uses any phylogenetic tree with meaningful branch lengths as an input and delimits OTUs on it by identification of branches whose removal significantly changes structure of the tree. Such branches are considered to reflect interspecific differentiation that is assumed generally more erratic than intraspecific branching. It is called branch-cutting method as it evaluates structural importance of the branch by its cutting (shrinking to zero length) and inspecting impact of this operation on the average pairwise distances between tree tips. Tree tips can be also constrained to be either conspecific or heterospecific which allows the method to achieve more robust and informed delimitations and to focus on particular phylogenetic scale. Usefulness of the method is demonstrated on four empirical examples and comparison with similar methods is performed.

evolutionary biology↗