Analysing Convergent Evolution: A Practical Guide to Methods
Convergent evolution, or the independent evolution of similar traits, has long been investigated and recognised as an important area of research for evolutionary biology. However, as with many areas of comparative biology, new phylogenetic methods that en
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Analysing Convergent Evolution: A Practical Guide to Methods Kevin Arbuckle and Michael P. Speed
Abstract Convergent evolution, or the independent evolution of similar traits, has long been investigated and recognised as an important area of research for evolutionary biology. However, as with many areas of comparative biology, new phylogenetic methods that enhance our ability to study convergence have arisen with greater frequency in recent years. Consequently, we now have a wide range of tools at our disposal and a rapidly developing conceptual framework to guide us in our analyses. This chapter aims to provide a practical guide for those interested in convergent evolution that will enable new entrants to the field to quickly develop a well-rounded research agenda. Although some methods can be performed in other pieces of (stand-alone) software, this guide will focus on the R statistical environment.
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Introduction
Convergent evolution is a common phenomenon across the diversity of living organisms. In essence, it refers to the independent evolution of some kind of similarity between two or more organisms, as opposed to any similarity which is a result of inheritance from a common ancestor. Convergent traits may be manifest across a number of levels of biology including both function and form (Losos 2011; Speed and Arbuckle 2016). Convergence can be seen for example in many forms of behaviour, morphology and physiology (McGhee 2011), and in the structure and action of molecules such as toxins or enzymes (Doolittle 1994). For instance, we could consider the phenomenon of mimicry, in which one organism (perhaps a harmless viceroy butterfly, Limenitis archippus) evolves to appear like a different K. Arbuckle (&) M.P. Speed Department of Ecology Evolution and Behaviour Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK e-mail: [email protected] M.P. Speed e-mail: [email protected] © Springer International Publishing Switzerland 2016 P. Pontarotti (ed.), Evolutionary Biology, DOI 10.1007/978-3-319-41324-2_2
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organism (such as a poisonous monarch butterfly, Danaus plexippus) in order to deceive another (e.g. a predator) and gain some advantage as a result (Cott 1940; Ruxton et al. 2004). A contrasting example to highlight the wide reach of convergence is the evolution of myoglobin with similar oxygen binding properties in the muscles of several aquatic mammal lineages, which enables prolonged diving ability (Mirceta et al. 2013). Convergence has long been considered as an important area of research in evolutionary biology. For example, in Chap. 6 of The Origin of Species, Darwin (1859) discussed several perceived difficulties with his theory of natural selection and invoked evolutionary convergence to counter some of these potential problems. More recently, convergence has been at the heart of modern comparative biology, albeit in an understated way. In particular, the power and applicability of phylogenetic comparative methods is t
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