The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies
The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies
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DOI：
10.1080/106351599260184
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发表时间：
1999-09-01
影响因子：
6.5
通讯作者：
Pagel, M
中科院分区：
文献类型：
--
作者：
Pagel, M
物种发生描述了一组物种从一个共同祖先遗传下来的等级模式。如果有关于骗局的特征状态的信息？临时物种，提出了使用该信息与生殖发生相结合来重建进化的历史事件的可能性。这些重建可以用来检索一幅世界的图片，随着物种的进化，沿着会是什么样子？来的分支的遗传学。这反过来又提供了一种检验进化和适应假说的方法。方法基于标准杆原理，simony重建祖先的性格状态，以尽量减少历史的数量？在本主题中观察到的产生多样性所需的性质变化？多孔物种（参见Maddison等人，1984年，为一般帐户）。Parsi的替代品？mony方法利用了princi？最大似然法。最大值？线性解使得观察到的数据最有可能给出被研究过程的某种模型（参见Edwards，1972）。在系统发育的背景下，这意味着侦察？构建祖先的特征状态，使当代物种中观察到的特征状态最有可能，给定一些进化方式的统计模型。最大似然解可能是也可能不是最简约解。我限制自己在这里使用最大似然模型来推断祖先的字符？字符状态的二进制离散字符，即字符只能采用两个国家，虽然推广到两个以上的国家需要没有新的CON？概念我的重建方法？tral states利用了一个马尔可夫模型的二进制字符演变的遗传（Pagel，1994）。Sanderson（1993）描述了一个相关的模型，用于研究假设祖先状态已知的字符的增益和损失率。Schluter（1995），Yang et al.（1995），以及Koshi和Goldstein（1996）推导出的方法与我将在这里描述的过程类似。然而，Yang et al.（1995）和Koshi和Goldstein（1996）使用我称之为”全局”的方法来估计祖先特征，我主张采用”局部”方法，因为全局方法不能产生对感兴趣的假设的最大似然估计。03 The Dog（1995）移植全球和当地的估计在他的？偶蹄类核糖核酸酶的研究，和Schluter et al.（1997年）报告的全球估计？
A phylogeny describes the hierarchical pattern of descent of some group of species from a common ancestor. If information is available on the character states of the con? temporary species, the possibility is raised of using that information in combination with the phylogeny to reconstruct the historical events of evolution. These reconstructions can be used to retrieve a picture of the world as the species evolved along what would be? come the branches of the phylogeny. This, in turn, provides a way to test hypotheses about evolution and adaptation. Methods based on the principle of par? simony reconstruct the ancestral character states to minimize the number of histori? cal character changes required to produce the diversity observed among the contem? porary species (see Maddison et al., 1984, for a general account). An alternative to parsi? mony approaches makes use of the princi? ple of maximum likelihood. Maximum like? lihood solutions make the observed data most likely given some model of the process under investigation (see Edwards, 1972). In a phylogenetic context this means recon? structing the ancestral character states to make the character states observed among the contemporary species most probable, given some statistical model of the way evolution proceeds. Maximum likelihood solutions may or may not be the most-parsimonious solution. I restrict myself here to using maximum likelihood models to infer ancestral char? acter states for binary discrete characters, that is, for characters that can adopt only two states, although the generalization to more than two states requires no new con? cepts. My approach to reconstructing ances? tral states makes use of a Markov model of binary character evolution on phylogenies (Pagel, 1994). Sanderson (1993) describes a related model for investigating rates of gains and losses of characters for which the ancestral states are assumed to be known. Schluter (1995), Yang et al.(1995), and Koshi and Goldstein (1996) derive methods that are similar to the procedures I will describe here. However, Yang et al.(1995) and Koshi and Goldstein (1996) use what I shall term" global" methods for estimating ancestral characters, I argue for a" local" approach on grounds that the global method does not produce a maximum-likelihood estimate of the hypothesis of interest. Schluter (1995) re? ported global and local estimators in his in? vestigation of artiodactyl ribonucleases, and Schluter et al.(1997) reported global estima?