Department of Ecology and Evolution, State University of New York at Stony Brook, 11794, USA.
Biol Rev Camb Philos Soc. 2012 Nov;87(4):991-1024. doi: 10.1111/j.1469-185X.2012.00240.x. Epub 2012 Aug 14.
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.
生物体中的所有特征和性状系统都具有共同的进化历史，可以使用系统发育方法进行估计。然而，由于改变的速率不同以及驱动这些速率的进化机制，普遍存在系统发育冲突。需要揭示这些驱动因素，因为进化过程与系统发育模型之间的不匹配会导致对错误假设的高度置信。随着字符和物种数量的快速扩展，基于形态与分子分析的系统发育之间以及基于不同分子序列子集的树之间的不匹配变得普遍存在。十多年来，从形态和分子数据推断出的新世界蝙蝠科 Phyllostomidae 成员之间的进化关系一直存在冲突。在这里，我们开发并应用了一些方法来最小化系统偏差，揭示系统发育冲突背后的生物学机制，并概述了未来基因组学和形态学数据收集的数据要求。我们为 Phyllostomidae 及其外群引入了新的形态学数据，并扩展了以前的分子分析，以消除系统发育冲突的方法学来源，例如分类采样、特征稀疏采样或使用不同的算法来估计系统发育。我们还评估了冲突的生物学来源的影响：形态变化和分子替换的饱和，以及导致不一致的树的其他过程，包括趋同的形态和分子进化。方法学来源的不匹配在产生系统发育冲突方面起着一定的作用，并且通过匹配分类单元、收集更多特征以及应用相同的算法来优化系统发育，相对容易消除。揭示的进化模式与多种冲突的生物学来源一致，包括形态和分子变化的饱和、花蜜喂养谱系之间的适应性形态趋同以及不一致的基因树。应用方法来解释核苷酸序列饱和可以减少，但不能完全消除 Phyllostomid 蝙蝠中系统发育冲突。我们排除了旁系同源、侧向基因转移以及在导致基因树不一致的过程中，在 Phyllostomid 蝙蝠中的祖先多态性的基因转移和分类单元选择。揭示和对抗祖先多态性的基因渗入和谱系分类对基因树的可能影响，需要在这个物种丰富的哺乳动物家族中，在基因组和等位基因测序方面取得巨大飞跃。我们还发现了在花蜜喂养谱系中，适应性分子进化导致线粒体蛋白趋同的证据。总之，产生系统发育冲突的生物学过程是普遍存在的，克服不匹配需要比已经在 Phyllostomid 蝙蝠等研究充分的生物中收集的更好的模型和更多的数据。
