Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum

Placozoa is an ancient phylum of extraordinarily unusual animals:
miniscule, ameboid creatures that lack most fundamental animal features.
Despite high genetic diversity, only recently have the second and third
species been named. While prior genomic studies suffer from incomplete
placozoan taxon sampling, we more than double the count with protein
sequences from seven key genomes and produce the first nuclear
phylogenomic reconstruction of all major placozoan lineages. This leads us
to the first complete Linnaean taxonomic classification of Placozoa, over
a century after its discovery: This may be the only time in the 21st
century when an entire higher taxonomy for a whole animal phylum is
formalized. Our classification establishes 2 new classes, 4 new orders, 3
new families, 1 new genus, and 1 new species, namely classes
Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea,
Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and
Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa,
nov. Our likelihood and gene content tree topologies refine the
relationships determined in previous studies. Adding morphological data
into our phylogenomic matrices suggests sponges (Porifera) as the sister
to other animals, indicating that modest data addition shifts this node
away from comb jellies (Ctenophora). Furthermore, by adding the first
genomic protein data of the exceptionally distinct and branching
Polyplacotoma mediterranea, we solidify its position as sister to all
other placozoans; a divergence we estimate to be over 400 million years
old. Yet even this deep split sits on a long branch to other animals,
suggesting a bottleneck event followed by diversification. Ancestral state
reconstructions indicate large shifts in gene content within Placozoa,
with Hoilungia hongkongensis and its closest relatives having the most
unique genetics.

扁盘动物门（Placozoa）是一类古老且极为奇特的动物类群：体型微小、呈变形虫状，缺失绝大多数基础动物特征。尽管该类群遗传多样性极高，但其第二、第三个物种直至近年才被正式命名。
此前的基因组研究均存在扁盘动物类群采样不全的问题，本研究通过七组关键基因组的蛋白质序列将已知物种数量翻倍有余，并首次完成了所有主要扁盘动物演化支的核基因组系统发育组学重建。
本研究在扁盘动物被发现一个多世纪后，首次建立了完整的林奈式分类体系——这或许是21世纪以来首次完整确立整个动物门的高阶分类系统。
本分类体系新增2个纲、4个目、3个科、1个属及1个物种，具体为：多板扁盘纲（Polyplacotomia）与单板扁盘纲（Uniplacotomia）；多板扁盘目（Polyplacotomea）、丝盘虫目（Trichoplacea）、分支扁盘目（Cladhexea）及洪氏扁盘目（Hoilungea）；多板扁盘科（Polyplacotomidae）、分支扁盘科（Cladtertiidae）及洪氏扁盘科（Hoilungidae）；以及分支扁盘属（Cladtertia），其模式种为合作分支扁盘虫（Cladtertia collaboinventa, nov.）。
本研究基于似然法与基因内容构建的系统发育树拓扑结构，优化了此前研究中得出的类群亲缘关系。
将形态学数据纳入系统发育组学矩阵后，分析结果显示海绵动物门（Porifera）为其余所有动物的姊妹群，这表明仅添加少量数据即可将该演化节点从栉水母动物门（Ctenophora）的位置修正过来。
此外，本研究首次发布了极具独特性且演化分支较早的地中海多板扁盘虫（Polyplacotoma mediterranea）的基因组蛋白质数据，明确了其作为所有其他扁盘动物姊妹群的演化位置，该分化事件距今估计已超过4亿年。
即便如此，该演化分支与其他动物类群间仍存在较长的演化枝长，这表明扁盘动物类群曾经历过瓶颈事件，随后才发生适应性辐射。
祖先状态重建分析显示，扁盘动物类群内部存在显著的基因内容演化变化，其中香港洪氏扁盘虫（Hoilungia hongkongensis）及其近缘类群拥有最为独特的遗传组成。