Species Delimitation in East African Cichlid Fish Adaptive Radiations

东非慈鲷适应性辐射的物种界定

• 批准号: 351201817
• 负责人: Professor Dr. Axel Meyer
• 金额: --
• 依托单位: School of Biology and Environmental Science
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2017
• 资助国家: 德国
• 起止时间: 2016-12-31 至 2023-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/351201817?language=en
• 关键词: Species; Delimitation; East; African; Cichlid

Taxonomy is necessary for documenting and understanding changes in biodiversity through time. To better discover, name, and quantify organismal diversity, we need better models and criteria for how to effectively and reproducibly integrate taxonomy with huge phylogenomic data sets. Only very recently have genomic and computational tools became available that permit taxonomists and systematists to establish robust taxonomic hypotheses also for extremely young species. Whole-genome de novo sequencing and re-sequencing (WGS) is becoming technically and financially feasible for more laboratories. This applies also to research on hyper-diverse and often extremely young East African adaptive radiations of cichlid fishes (genome sizes =< 1Gb). The species flocks in Lake Victoria are particularly young (500 species arose in probably less than 12,000 years) whereas those of Lake Malawi (800-1000 species that are 2-4 MYA) are of intermediate age compared to the much older lineages of Lake Tanganyika (250 species that are up to 8-10MYA). Hybridization, incomplete lineage sorting, and the retention of ancient polymorphisms all contribute to gene/allele trees not agreeing with species trees. These phenomena are believed to be particularly onerous among the younger species, but less problematic for the older species of Lake Tanganyika. We plan to re-sequence (reference genomes are available) about 200 cichlid genomes of systematically chosen species pairs from each of the three radiations (25 individuals per species to be able to discover alleles at 5% frequency). These vast amounts of sequence data also cause novel challenges on how to elucidate the relationships between evolutionary processes and how genetic variation is distributed among lineages and species. The diagnoses of new taxa in the genomic age will demand phylogenomic analyses that account for the interplay between processes that affect genome architecture, interspecific gene flow, and the time-scales for speciation. Using entire genomes we plan to explore, partition, and analyze these data in an effort to develop more objective and reproducible taxonomic criteria based on particular molecular marker sets. The WGS data will be analyzed in full and also in several partitioned data sets whose congruence between gene and species trees will be evaluate through analyses including Structure, PCA, and Bayesian statistical methods, with the aim to devise rules for taxon diagnosis that, of course, are expected to apply not only for cichlids.

分类学对于记录和理解生物多样性随时间的变化是必要的。为了更好地发现、命名和量化生物多样性，我们需要更好的模型和标准来有效地、可重复地将分类学与庞大的基因组数据集整合起来。直到最近，基因组学和计算工具才出现，使分类学家和系统分类学家能够为非常年轻的物种建立可靠的分类学假设。全基因组从头测序和重新测序（WGS）对于更多的实验室来说在技术上和财政上都是可行的。这也适用于研究超多样性和往往非常年轻的东非适应辐射的慈鲷鱼（基因组大小=< 1Gb）。维多利亚湖的物种群特别年轻（500个物种可能在不到12，000年的时间内出现），而马拉维湖的物种群（800- 1，000个物种，2-4百万年）与坦噶尼喀湖的更古老的谱系（250个物种，长达8- 10百万年）相比处于中间年龄。杂交、不完全的谱系分类和古老多态性的保留都导致基因/等位基因树与物种树不一致。据信，这些现象在较年轻的物种中特别严重，但对坦噶尼喀湖的较老物种来说问题较小。我们计划重新测序（参考基因组可用）约200个慈鲷基因组的系统选择的物种对从每三个辐射（25个个体，每个物种能够发现等位基因在5%的频率）。这些大量的序列数据也对如何阐明进化过程之间的关系以及遗传变异如何在谱系和物种之间分布提出了新的挑战。在基因组时代，新类群的诊断将需要大量的基因组分析，解释影响基因组结构，种间基因流和物种形成的时间尺度的过程之间的相互作用。使用整个基因组，我们计划探索，分区和分析这些数据，努力发展更客观和可重复的分类标准的基础上，特定的分子标记集。WGS数据将进行全面分析，也在几个分区的数据集，其基因和物种树之间的一致性将通过分析，包括结构，PCA和贝叶斯统计方法进行评估，目的是设计规则分类诊断，当然，预计不仅适用于慈鲷。