Reconstructing the Tree of Life: Are molecular phylogenies really better than morphological ones?

进化趋同现象对进化的可预测性有着有趣的影响（https：//theconvolution.com/what-do-aliens-look-like-the-clue-is-inevolution-63899）。然而，它往往使准确重建进化关系变得困难。特别是，人们经常假设，趋同是一个特别困扰形态学进化的问题，使它们不那么准确（http：//www.42evolution.org/videos/researcher/professor-matthew-wills/），但这真的是这样吗？从分子数据中生成系统发育树越来越容易，分析可以将数十个或数百个基因的序列串联起来。尽管新的分子树有着丰富的数据基础，但它们往往包含着令人惊讶的东西，并且经常暗示着与从形态学数据中得出的既定和传统假设不一致的关系。一个这样的例子是哺乳动物目的进化：“新哺乳动物的进化”推翻了许多“传统”的类群（图1）。另一个例子是节肢动物。我们如何看待这些冲突？我们是否必须得出结论，新的分子树可能是正确的;被大量的分子数据和更复杂的分析模型所动摇？这样做意味着几十年的比较解剖学和形态学研究已经产生了数据，这些数据充其量只是比分子数据更嘈杂和更容易出错。在最坏的情况下，它可能表明形态学数据的趋同性意味着肯定会产生误导的关系。由于不可能确切地知道同源性，因此不可能有准确性的客观检验。然而，它是可能的，以评估的一致性与独立来源的数据进化历史的竞争树。首先，在地层首次出现日期的终端（种，属和更高的类群）是已知的合理的准确性，隐含的鬼谱系的程度（相对于理论的限制）提供了一个指数的“拟合优度”的化石记录。第二，许多类群的地理或古生物地理分布包含一个剩余的进化信号，这也可以检验它是否适合于竞争树。虽然地层学和地理学都不一定能在任何特定情况下提供万无一失的区分，但它们对大量统计样本的应用--不同的主要分支、不同的分类水平、不同的辐射年龄--允许某种程度的普遍性。该项目还将确定哪些分支在哪些情况下最容易发生形态学趋同，因此最适合用分子数据进行分析。学生将获得跨学科和可转移的技能：生物信息学，遗传学，统计学和古生物学。

The phenomenon of evolutionary convergence has intriguing implications for the extent to whichevolution may be predictable (https://theconversation.com/what-do-aliens-look-like-the-clue-is-inevolution-63899).However, it often makes it difficult to reconstruct evolutionary relationships withaccuracy. In particular, it is often assumed that convergence is a problem that particularly bedevilsmorphological phylogenies, making them less accurate(http://www.42evolution.org/videos/researcher/professor-matthew-wills/), but is this really thecase?It is increasingly easy to generate phylogenetic trees from molecular data, with analyses routinelyconcatenating sequences from many tens or hundreds of genes. Despite their data-richunderpinnings, new molecular trees often contain surprises, and frequently imply relationships thatare at odds with established and traditional hypotheses derived from morphological data. One suchexample is the phylogeny of mammal orders: the 'new mammal phylogeny' overturns many'traditional' groups (Fig. 1). Another example is the arthropods. How are we to view these conflicts?Should we necessarily conclude that the new molecular trees are likely to be the correct ones; swayedby the mass of molecular data and greater complexity of analytical models? To do so implies that manydecades of comparative anatomy and morphological scholarship have yielded data that are - at best- simply more noisy and error prone than the data from molecules. At worst, it may indicate thatconvergence within morphological data implies relationships that are positively misleading.Since phylogeny cannot be known with certainty, there can be no objective test of accuracy. However,it is possible to assess the congruence of competing trees with independent sources of data onevolutionary history. Firstly, where the stratigraphic first occurrence dates of terminals (species,genera and higher taxa) are known with reasonable accuracy, the extent of implied ghosts lineages(relative to theoretical limits) offers an index of the 'goodness of fit' to the fossil record. Secondly, thebiogeographical or palaeobiogeographical distributions of many groups contain a residualevolutionary signal, and this can also be tested for its fit to competing trees. While neither stratigraphynor biogeography necessarily offers foolproof discrimination in any particular case, their applicationto a large statistical sample of cases - different major clades, different taxonomic levels, different agesof radiations - allows for some level of generality. The project will also identify which clades underwhich circumstances are most prone to morphological convergence, and therefore most suitablyanalysed with molecular data.The student will acquire an interdisciplinary and transferrable skill set: bioinformatics, phylogenetics,statistics and palaeontology.