长期持有的关于动物进化亲缘关系的理念最近已被时有争议的主要基于源自分子数据的见解的假说所颠覆。这些新假设包括：蜕皮动物的一个类群（蜕皮动物门）以及触手冠类动物（一种已绝种的无脊椎动物）与软体动物和环节动物（冠轮动物门）的密切亲缘关系。包括那些需要使性状系统发育进化关键特征极化的关系在内的许多亲缘关系仍具有争议，且对深节点的支持呼声往往较低。使用来自许多基因的数据的分子系统学方法已致力于探清动物间深远的亲缘关系，但因缺乏许多重要群体的数据而受阻。在这里，我们报告了总共39.9 MB隶属21类门下29种动物的表达序列标签（其中包括之前缺乏基因或已表达序列标签数据的11类门）。在与现有序列进行共同分析后，我们的数据验证了部分以前发现的已在动物树中彻底分化的类群（包括原口动物门，蜕皮动物门和冠轮动物门）并明确解决了一系列存在已久的争议，这些争议在只持有较少数据的早期研究中曾得到分歧方的大力支持。（如将天鹅绒虫而非缓步动物门划分为节肢动物的姊妹类群），而且还为软体动物单系这一早经形态学家鉴定通过的类群提供了分子层面的支持。此外，我们还为 某些新兴假设找到了有力支持。这其中包括将环节动物，纽虫，帚虫类和腕足类归为同类的一个分支（包括星虫和螠虫），将软体动物归为该组合的姊妹类群，以及将栉水母划分为最早分化的现存多细胞动物。且通过受有利支持的节点，我们推断出了螺旋卵裂的单一起源（伴随着随后损耗）。许多类群稳定子集间的关系得到了强有力的支持，亲缘谱系数量的日益减少使得对进化树的完善仍显棘手。
Abstract
Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combina- tion with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combina- tion with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.