Phylogeny of panpulmonate gastropods investigated using a 'reduced-representation' genomic approach

使用“减少代表性”基因组方法研究泛肺腹足动物的系统发育

• 批准号: 243478344
• 负责人: Professor Dr. Michael Schrödl
• 金额: --
• 依托单位: Leibniz-Institut zur Analyse des Biodiversitätswandels (LIB)
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2013
• 资助国家: 德国
• 起止时间: 2012-12-31 至 2015-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/243478344?language=en
• 关键词: Phylogeny; panpulmonate; gastropods; investigated; using

Analyses using transcriptomic sequence data are revolutionizing deep molluscan phylogeny. Generating whole genomes or expressed sequence tags (ESTs) still is, however, relatively costly and becomes less efficient for shallower phylogenetic levels with rapidly increasing taxon diversity. There is thus a persisting lack of molecular markers available to test novel hypotheses on subgroups. According to our 4-gene analyses, the inner topology and evolution of euthyneuran gastropods, representing roughly 50,000 species, radically differs from traditional concepts. Our recently established taxon Panpulmonata is diverse with regard to species numbers, morphology and biology, comprising a mix of traditional opisthobranch and pulmonate orders, and some enigmatic snail taxa. Mitochondrial gene trees contradicted such a new topology, while EST-based topologies have given local support. Urgent questions remain, i.e. whether or not there is a new euthyneuran tree with monophyletic Panpulmonata, how internal panpulmonate evolution was, and how to resolve the phylogeny of hyperdiverse taxa reliably and efficiently.Newly developed reduced representation genomic approaches using double digest Restriction-Site Associated DNA sequencing (ddRADseq) can generate thousands of independent nuclear genomic sequence markers for hundreds of samples in parallel, i.e. quickly and at very low costs per sample. In the herein proposed project, we want to explore and establish the use of ddRADseqs as phylogenetic markers, from shallow to deeper levels, within the framework of clarifying panpulmonate phylogeny and evolution. We apply for consumables generating more than 1000 ddRADseqs using available DNA from more than 1000 different euthyneurans. This includes an almost complete species sampling of global acochlidians, covers roughly half of the known panpulmonate families with multiple representatives, and considers all relevant major outgroup taxa. Already in the pilot phase of the project applied for herein, i.e. the first 18 months of funding, we hope for robust results, 1) testing the debated monophyly of Panpulmonata and resolving its origin, 2) reconstructing panpulmonate ordinal and family-level phylogeny (excluding most stylommatophorans), 3) resolving the origin and inner evolution of acochlidians, compared to available multi-locus and morphology-based trees. We will apply state of the art phylogenetic and evolutionary analyses, but also perform up-to-date molecular species delimitation approaches. With our massif genomic data (> 300,000 bp per sample) across many subtaxa we will evaluate current paradigms on character evolution and macro-evolutionary patterns among panpulmonates, such as the invasions of terrestrial and limnic systems.

利用转录组序列数据进行分析正在彻底改变深层软体动物的系统发育。然而，生成全基因组或表达序列标签（est）仍然是相对昂贵的，并且随着分类单元多样性的迅速增加，在较浅的系统发育水平上变得效率较低。因此，一直缺乏可用的分子标记来测试对亚群的新假设。根据我们的4基因分析，代表大约5万个物种的euthyneuran腹足类动物的内部拓扑结构和进化与传统概念有根本不同。我们最近建立的分类群Panpulmonata在物种数量、形态和生物学上都很多样化，包括传统的蛇门目和肺门目，以及一些神秘的蜗牛分类群。线粒体基因树与这种新的拓扑结构相矛盾，而基于est的拓扑结构则提供了局部支持。是否存在一种新的单系泛肺纲的euthyneuran树，泛肺纲内部是如何进化的，以及如何可靠有效地解决高多样性分类群的系统发育问题仍然是亟待解决的问题。新开发的使用双酶切限制性位点相关DNA测序（ddRADseq）的减少代表性基因组方法可以同时为数百个样品生成数千个独立的核基因组序列标记，即快速且每个样品的成本非常低。在本文提出的项目中，我们希望在阐明泛肺动物系统发育和进化的框架内，从浅层到深层探索和建立ddRADseqs作为系统发育标记的使用。我们申请使用来自1000多个不同的神经细胞的可用DNA产生超过1000个ddradseq的消耗品。这包括一个几乎完整的物种样本，覆盖了大约一半的已知的有多个代表的泛肺纲科，并考虑了所有相关的主要外群分类群。本项目已经进入了试点阶段，即前18个月的资助，我们希望能够获得可靠的结果，1)测试有争议的Panpulmonata单系并解决其起源问题，2)重建Panpulmonata有序和家族水平的系统发育（不包括大多数柱头虫），3)与现有的多位点和基于形态的树相比，解决acochlidian的起源和内部进化问题。我们将应用最先进的系统发育和进化分析，同时也执行最新的分子物种划分方法。利用我们在许多亚类群中的大量基因组数据（每个样本300,000 bp），我们将评估泛肺动物的特征进化和宏观进化模式的当前范式，例如陆地和湖泊系统的入侵。

项目成果

Exploring the Diversity of Mesopsammic Gastropods: How to Collect, Identify, and Delimitate Small and Elusive Sea Slugs?*

探索中栖腹足类动物的多样性：如何收集、识别和界定小型且难以捉摸的海蛞蝓？*

• DOI: 10.4003/006.032.0205
• 发表时间: 2014
• 作者: Jörger;Neusser;Brenzinger;Schrödl
• 通讯作者: Schrödl

Revised Classification, Nomenclator and Typification of Gastropod and Monoplacophoran Families

• DOI: 10.4002/040.061.0201
• 发表时间: 2017-12
• 期刊: Malacologia
• 影响因子: 1.3
• 作者: P. Bouchet;J. Rocroi;B. Hausdorf;A. Kaim;Y. Kano;A. Nützel;P. Parkhaev;M. Schrödl;E. Strong

Life on a leaf: 3D-reconstruction and description of a new limapontiid sacoglossan (Gastropoda: Heterobranchia: ‘Opisthobranchia’) living on the seagrass Halophila ovalis

叶子上的生命：生活在海草 Halophila ovalis 上的新 limapontiid sacoglossan（腹足纲：异鳃亚纲：“Opisthobranchia”）的 3D 重建和描述

• DOI: 10.1093/mollus/eyu071
• 发表时间: 2014
• 期刊: Journal of Molluscan Studies
• 影响因子: 1.2
• 作者: Jensen;Kohnert;Bendell;Schrödl
• 通讯作者: Schrödl