Authors:	Pirie, Michael
Title:	Inferring species trees given coalescence and reticulation
Online publication date:	14-Jun-2017
Year of first publication:	2017
Language:	english
Abstract:	Hybridisation is an important process in plant evolution, its impact apparent at all levels from the genome duplications shared by all angiosperms through to recent speciation events. Patterns of inheritance caused by hybridisation (and other reticulate processes) appear to be incompatible with one of the fundamental tools of evolutionary biologists and ecologists seeking to understand the evolution of biological diversity: the phylogenetic tree. The current paradigm for inferring relatedness of organisms – the ‘species tree’ – can be summed up in one word: coalescence. Current analytical approaches serve to bias against inferring reticulate processes, even though they may be common and of direct importance both for the evolutionary process itself and for the performance of methods used to infer it. I present a brief account of current methodologies and draw on examples from both plant and virus datasets to illustrate the importance of reticulate processes in evolutionary inference. An example from danthonioid grasses shows how our inference of the direction and frequency of long distance dispersal events can be impacted by post-dispersal hybridisation; one from the northern heathers (genus Erica) shows the impact on interpretations of morphological evolution. In viruses, recombination can lead to pathogenic strains, and our ability to infer this process, even on human timescales, is dependent on correctly interpreting differences between gene trees. I illustrate an easily implemented approach that may be used to infer the sequence and timing of gene and genome divergences given conflict between individual gene trees, even when the processes underlying that conflict cannot be distinguished. It can in principle be applied to any group of organisms and can be extended to explicitly model both reticulation and coalescence without prior knowledge of the species tree topology.
DDC:	580 Pflanzen (Botanik) 580 Botanical sciences
Institution:	Johannes Gutenberg-Universität Mainz
Department:	FB 10 Biologie
Place:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-468
URN:	urn:nbn:de:hebis:77-publ-567745
Version:	Original work
Publication type:	Habilitationsschrift
License:	In Copyright
Information on rights of use:	https://rightsstatements.org/vocab/InC/1.0/
Extent:	48 S.
Appears in collections:	JGU-Publikationen