A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life history evolution

Platyhelminthes (flatworms) are a diverse invertebrate phylum that are useful for exploring life history evolution. Within Platyhelminthes, only two clades develop through a larval stage: free-living polyclads and parasitic neodermatans. Neodermatan larvae are considered evolutionarily derived, whereas polyclad larvae are hypothesized to be retained from the last common ancestor of Platyhelminthes – and Spiralia – due to ciliary band similarities among polyclad and other spiralian larvae. However, larval evolution has been challenging to investigate within polyclads due to low support for deeper phylogenetic relationships. To investigate polyclad life history evolution, we generated transcriptomic data for 21 species of polyclads to build a well-supported phylogeny for the group. We then used ancestral state reconstruction to investigate ancestral modes of development (direct vs indirect) within Polycladida, and flatworms in general. The resulting tree provides strong support for deeper..., Quality control and assembly of reads
Reads that failed to pass the Illumina “Chastity” quality filter were excluded from our analyses. Reads passing the quality filter were assembled using Trinity (version 2.4.0 for most, but version 2.6.6 for species Boninia divae and Theama mediterranea; (Grabherr et al. 2011)) with default settings, which required assembled transcript fragments to be at least 200 bp in length. Reads were trimmed pre-assembly for the species Boninia divae and Theama mediterranea using Trimmomatic (Bolger, Lohse, and Usadel 2014).
Orthology assignment
Translated transcript fragments were organized into orthologous groups corresponding to a custom platyhelminth-specific core-ortholog set of 9,157 protein models (constructed in the same manner as in (Goodheart et al. 2015)) using HaMStR (version 13.2.6; (Ebersberger, Strauss, and von Haeseler 2009)), which in turn used FASTA (version 36.3.6; (Pearson and Lipman 1988)), GeneWise (version 2.2.0; (Birney, Clamp, and Durbin...,

扁形动物门（Platyhelminthes，又称扁形动物（flatworms））是一类多样性丰富的无脊椎动物门，在探究生活史演化领域具有重要研究价值。在扁形动物门内，仅两个演化支拥有幼虫阶段发育过程：自由生活的多歧肠类（polyclads）与寄生的新皮动物类（neodermatans）。新皮动物类的幼虫被认为是演化衍生类群，而基于多歧肠类幼虫与其他螺旋动物幼虫的纤毛带结构相似性，学界推测多歧肠类幼虫是扁形动物门——乃至螺旋动物总门（Spiralia）——的最近共同祖先所保留的发育特征。然而，由于深层系统发育关系的支持度较低，多歧肠类的幼虫演化研究长期以来面临诸多挑战。
为探究多歧肠类的生活史演化，本研究对21种多歧肠类动物生成转录组数据，以构建该类群具有高支持度的系统发育树；随后通过祖先状态重建（ancestral state reconstruction），分别解析多歧肠目（Polycladida）乃至整个扁形动物的祖先发育模式（直接发育与间接发育）。本研究构建的系统发育树为深层系统发育关系提供了强有力的支持……
### 测序读段的质控与组装流程
未通过Illumina "Chastity" 质控过滤的读段被剔除出本研究分析流程。通过质控的读段采用Trinity（多数样本使用版本2.4.0，Boninia divae与Theama mediterranea两个物种使用版本2.6.6；Grabherr等，2011）以默认参数进行组装，要求组装得到的转录本片段长度不低于200碱基对（bp）。其中，针对Boninia divae与Theama mediterranea，研究人员在组装前使用Trimmomatic（Bolger、Lohse与Usadel，2014）对读段进行剪切质控。
### 直系同源归类
将翻译得到的转录本片段按照自定义的扁形动物特异性核心直系同源基因集（包含9157个蛋白模型，构建方式与Goodheart等，2015的研究一致）进行直系同源分组，该分析使用HaMStR（版本13.2.6；Ebersberger、Strauss与von Haeseler，2009）工具，而HaMStR底层调用了FASTA（版本36.3.6；Pearson与Lipman，1988）与GeneWise（版本2.2.0；Birney、Clamp与Durbin……