![]() Ordered characters can be placed in an order so that transitions only occur between adjacent states. For characters with more than two states, there is a key distinction between ordered and unordered characters. We will consider discrete characters where each species might exhibit one of k states. For example, how many times this character has changed in the evolutionary history of squamates? How often does limblessness evolve? Do limbs ever re-evolve? Is the evolution of limblessness related to some other aspect of the lives of these reptiles? We might have particular questions about the evolution of limblessness in squamates. For limblessness in squamates, each species is either legless (state 0) or not (state 1 actually, there are some species that might be considered “intermediate” Brandley et al. However, many characters of interest to biologists are best defined as characters with a set number of fixed states. So far, we have only dealt with continuously varying characters. Section 7.2: Modeling the evolution of discrete states Fitting this model to comparative data will help us understand the evolution of traits like limblessness where species can be placed into one of a number of discrete character states. In this chapter, I will discuss the Mk model (Lewis 2001), which is a general approach to modeling the evolution of discrete traits on trees. Analyzing the evolution of discrete traits requires a different modeling approach than what we used for continuous traits. Limblessness is an example of a discrete trait – a trait that can occupy one of a set of distinct character states. User:Marek_bydg / Wikimedia Commons / CC-BY-SA-3.0. User:Smacdonald / Wikimedia Commons / CC-BY-SA-2.5, F. User:Bladerunner8u / Wikimedia Commons / CC-BY-SA-3.0, E. User:Gionorossi / Wikimedia Commons / CC-BY-SA-4.0, D. Photo credits: A: User:Raul654 / Wikimedia Commons / CC-BY-SA-3.0, B. Figure 7.1E and F), with some estimates that squamates have lost their limbs at least 26 times in the past 240 million years (Brandley et al. In fact, lineages within squamates have lost their limbs over and over again through their history (e.g. And snakes are not the only limbless lineage of squamates. ![]() In other words, snakes are lizards – highly modified lizards, but lizards nonetheless. 2006) – and also underwent a suite of changes to their head shape, digestive tract, and other traits associated with their limbless lifestyle. The squamate lineage that is ancestral to snakes became limbless about 170 million years ago (see Hedges et al. Even the snakes (Figure 7.1C and D), extraordinarily diverse in their own right (~3,500 species), are actually a clade that is nested within squamates (Streicher and Wiens 2017). From the gigantic Komodo dragon of Indonesia (Figure 7.1A, Varanus komodoensis) to tiny leaf chameleons of Madagascar (Figure 7.1B, Brookesia), squamates span an impressive range of form and ecological niche use (Vitt et al. Squamates, the clade that includes all living species of lizards, are well known for their diversity. Frameworkĭiscrete values (e.g.R markdown to recreate analyses Chapter 7: Models of discrete character evolution Section 7.1: Limblessness as a discrete trait The links to papers in the "BEAST 2.x" column are to the paper that describes the implementation of the model in the BEAST framework. The "Model reference" is the citation for the original description of the model (not necessarily in a Bayesian context). Yellow means the method has either not yet been published in a peer-reviewed journal, or that it has been implemented (and perhaps published) but not extensively tested for general use. Green means the model has been published and extensively tested. For ease of comparison BEAST 1.8 is also included, but you should consult the BEAST1 website for definitive information about that version of the platform, as keeping this table up-to-date is rather challenging. The tables below list the main evolutionary models supported by BEAST 2.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |