Species Delimitation in East African Cichlid Fish Adaptive Radiations

分类学对于记录和了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，以便有效和可重复地将分类学与巨大的系统基因组数据集相结合。直到最近，基因组和计算工具才出现，使分类学家和系统学家能够为非常年轻的物种建立健全的分类学假说。全基因组从头测序和再测序(WGS)在技术上和经济上对更多的实验室来说都是可行的。这也适用于对东非极端多样化和通常是非常年轻的慈鱼的适应性辐射的研究(基因组大小=1 GB)。维多利亚湖的种群特别年轻(500个物种出现在可能不到12,000年的时间里)，而马拉维湖的种群(800-1000个物种，2-4个MYA)与坦噶尼喀湖更古老的谱系(250个物种，8-10个MYA)相比，是中等年龄的。杂交、不完全的谱系分类和保留古老的多态都会导致基因/等位基因树与物种树不一致。这些现象被认为在较年轻的物种中尤其严重，但对于坦噶尼喀湖的较老物种来说问题较小。我们计划从三次辐射中的每一次中系统地选择物种对(每个物种25个个体，以便能够以5%的频率发现等位基因)重新排序(可获得参考基因组)。这些海量的序列数据也带来了新的挑战，即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。在基因组时代对新分类群的诊断将需要系统基因组学分析，以说明影响基因组结构、种间基因流动和物种形成的时间尺度的过程之间的相互作用。利用整个基因组，我们计划探索、划分和分析这些数据，以努力开发基于特定分子标记集的更客观和可重复性的分类标准。WGS数据将被完整地分析，也将在几个分割的数据集中进行分析，这些数据集的基因和物种树之间的一致性将通过包括结构、主成分分析和贝叶斯统计方法在内的分析来评估，目的是制定分类单元诊断的规则，当然，这些规则预计不仅适用于葫芦科。

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.