Understanding phylogenetic incongruence: lessons from phyllostomid bats.
Understanding phylogenetic incongruence: lessons from phyllostomid bats.
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DOI：
10.1111/j.1469-185x.2012.00240.x
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发表时间：
2012-11
影响因子：
--
通讯作者：
Simmons NB
中科院分区：
文献类型：
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作者：
Dávalos LM;Cirranello AL;Geisler JH;Simmons NB
生物体中的所有性状和性状系统都有一个共同的进化历史，可以用系统发育方法进行估计。然而，不同的变化速率和进化机制驱动这些速率导致普遍的系统发育冲突。这些驱动因素需要被发现，因为进化过程和系统发育模型之间的不匹配可能导致不正确假设的高置信度。由于数据集在性状和物种方面都迅速扩大，来自形态学与分子分析的同源性之间以及基于不同分子序列子集的树之间的不一致性变得普遍。十多年来，从形态学和分子数据推断的新世界蝙蝠家族Phyllostomidae成员之间的进化关系一直存在冲突。在这里，我们开发和应用的方法，以尽量减少系统偏差，揭示系统发育冲突的生物学机制，并概述未来的基因组和形态学数据收集的数据要求。我们引入了新的形态学数据phyllostomids和外类群，并扩大以前的分子分析，以消除系统发育冲突的方法来源，如分类采样，稀疏字符采样，或使用不同的算法来估计的系统发育。我们还评估了冲突的生物来源的影响：形态变化和分子取代的饱和度，以及导致不一致的树，包括收敛的形态和分子进化的其他过程。不一致的方法学来源在产生系统发育冲突中发挥了一定的作用，并且相对容易通过匹配分类群，收集更多的特征，并应用相同的算法来优化系统发育来消除。揭示的进化模式是一致的，与多个生物来源的冲突，包括饱和的形态和分子变化，自适应形态之间的收敛花蜜喂养谱系，和不一致的基因树。应用方法来解释核苷酸序列饱和度减少了，但并没有完全消除，系统发育冲突。我们排除了paralogy，横向基因转移，和穷人的分类单元采样和外群选择的过程中，导致不一致的基因树在phyllostomid蝙蝠。揭示和对抗基因树上祖先多态性的渐渗和谱系排序的可能影响，将需要在这个物种丰富的哺乳动物家族中的基因组和等位基因测序的巨大飞跃。我们还发现了自适应分子进化的证据，导致收敛的线粒体蛋白之间的花蜜喂养谱系。总之，产生系统发育冲突的生物过程是无处不在的，克服不一致需要更好的模型和更多的数据，即使是在研究充分的生物体，如叶口虫蝙蝠。
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.