An unbiased molecular approach using 3’UTRs resolves the avian family-level tree of life

Presumably, due to a rapid early diversification, major parts of the
higher-level phylogeny of birds are still resolved controversially in
different analyses or are considered unresolvable. To address this
problem, we produced an avian tree of life, which includes molecular
sequences of one or several species of ∼ 90% of the currently recognized
family-level taxa (429 species, 379 genera) including all 106 for the
non-passerines and 115 for the passerines (Passeriformes). The
unconstrained analyses of noncoding 3-prime untranslated region (3’UTR)
sequences and those of coding sequences yielded different trees. In
contrast to the coding sequences, the 3’UTR sequences resulted in a
well-resolved and stable tree topology. The 3’UTR contained, unexpectedly,
transcription factor binding motifs that were specific for different
higher-level taxa. In this tree, grebes and flamingos are the sister clade
of all other Neoaves, which are subdivided into five major clades. All
non-passerine taxa were placed with robust statistical support including
the long-time enigmatic hoatzin (Opisthocomiformes), which was found being
the sister taxon of the Caprimulgiformes. The comparatively late radiation
of family-level clades of the songbirds (oscine Passeriformes) contrasts
with the attenuated diversification of non-passeriform taxa since the
early Miocene. This correlates with the evolution of vocal production
learning, an important speciation factor, which is ancestral for songbirds
and evolved convergent only in hummingbirds and parrots. Since 3’UTR-based
phylotranscriptomics resolved the avian family-level tree of life, we
suggest that this procedure will also resolve the all-species avian tree
of life

推测而言，由于早期快速分化，鸟类高级阶元系统发育的主要部分在不同分析中仍存在争议，或被认为无法解析。为解决这一问题，我们构建了一棵鸟类生命之树，包含当前已确认的约90%科级分类单元（共429种、379属）中一个或多个物种的分子序列，其中非雀形目（non-passerines）全部106科、雀形目（Passeriformes）115科均被涵盖。对非编码3'非翻译区（3'UTR）序列和编码序列的无约束分析得到了不同的树拓扑结构。与编码序列相比，3'UTR序列得到了分辨率高且稳定的树拓扑结构。意外的是，3'UTR包含了针对不同高级阶元分类单元的转录因子结合基序（transcription factor binding motifs）。在此树中，鸊鷉与火烈鸟构成所有其他新鸟亚纲（Neoaves）类群的姐妹支，而新鸟亚纲又被划分为五个主要分支。所有非雀形目分类单元均获得强烈的统计支持，包括长期以来分类地位不明的麝雉（Opisthocomiformes）——其被发现是夜鹰目（Caprimulgiformes）的姐妹类群。鸣禽（鸣雀形目，oscine Passeriformes）科级分支的相对较晚辐射分化，与早中新世以来非雀形目类群减弱的分化形成对比。这与发声学习（vocal production learning）的演化相关——发声学习是一个重要的物种形成因素，为鸣禽的祖先特征，且仅在蜂鸟和鹦鹉中发生趋同演化。鉴于基于3'UTR的系统转录组学（3'UTR-based phylotranscriptomics）成功解析了鸟类科级生命之树，我们认为该方法也将能解析包含所有物种的鸟类生命之树。