Data from: The pipid root

The estimation of phylogenetic relationships is an essential component of understanding evolution. Accurate phylogenetic estimation is difficult, however, when internodes are short and old, when genealogical discordance is common due to large ancestral effective population sizes or ancestral population structure, and when homoplasy is prevalent. Inference of divergence times is also hampered by unknown and uneven rates of evolution, the incomplete fossil record, uncertainty in relationships between fossil and extant lineages, and uncertainty in the age of fossils. Ideally these challenges can be overcome by developing large “phylogenomic” datasets, and by analyzing them with methods that accommodate features of the evolutionary process such as genealogical discordance, recurrent substitution, recombination, ancestral population structure, gene flow after speciation among sampled and unsampled taxa, and variation in evolutionary rates. In some phylogenetic problems it is possible to use information that is independent of fossils, such as the geological record, to identify putative triggers for diversification whose associated estimated divergence times can then be compared a posteriori to estimated relationships and ages of fossils. The history of diversification of pipid frog genera Pipa, Hymenochirus, Silurana, and Xenopus, for instance, is characterized by many of these evolutionary and analytical challenges. These frogs diversified dozens of millions of years ago, they have a relatively rich fossil record, their distributions span continental plates with a well characterized geological record of ancient connectivity, and there is considerable disagreement across studies in estimated evolutionary relationships. We used high throughput sequencing and public databases to generate a large phylogenomic dataset with which we estimated evolutionary relationships using multilocus coalescence methods. We collected sequence data from Pipa, Hymenochirus, Silurana, and Xenopus and the outgroup taxon Rhinophrynus dorsalis from coding sequence of 113 autosomal regions, averaging ~300 base pairs in length (range: 102 – 1695 base pairs), and also a portion of the mitochondrial genome. Analysis of these data using multiple approaches recovers strong support for the ((Xenopus, Silurana)(Pipa, Hymenochirus)) topology, and geologically calibrated divergence time estimates that are consistent with estimated ages and phylogenetic affinities of many fossils. These results provide new insights into the biogeography and chronology of pipid diversification during the breakup of Gondwanaland, and illustrate how phylogenomic data may be necessary to tackle tough problems in molecular systematics.

系统发育关系的推断是解析演化过程的核心环节。然而，在以下场景中精准的系统发育推断极具挑战：支间间隔短且古老、因祖先有效种群规模庞大或祖先种群结构普遍存在谱系不协和现象、以及同塑性（homoplasy）广泛出现。分化时间的推断同样面临诸多阻碍：演化速率未知且不均一、化石记录不完整、化石与现生支系间的亲缘关系存在不确定性、以及化石年代的判定存在误差。理想情况下，这些难题可通过构建大型系统基因组数据集（phylogenomic datasets），并采用适配演化过程特征的分析方法加以解决——这类特征包括谱系不协和（genealogical discordance）、反复替换（recurrent substitution）、重组（recombination）、祖先种群结构、物种形成后采样类群与未采样类群间的基因流（gene flow），以及演化速率异质性。

在部分系统发育研究场景中，可借助独立于化石的信息（如地质记录）识别推测的多样化触发因素，随后将其估算的分化时间与化石的亲缘关系及年代估算结果进行后验比对。例如，负子蟾科各属——包括负子蟾属（Pipa）、拟爪蟾属（Hymenochirus）、Silurana属与爪蟾属（Xenopus）——的演化多样化历史，就兼具上述诸多演化与分析层面的挑战。这类蛙类的分化发生于数千万年前，拥有相对丰富的化石记录，其分布跨越了古大陆连接史研究较为透彻的大陆板块，且不同研究间估算的演化亲缘关系存在显著分歧。

本研究借助高通量测序与公共数据库构建了一套大型系统基因组数据集，并采用多位点溯祖方法估算演化亲缘关系。我们从负子蟾属（Pipa）、拟爪蟾属（Hymenochirus）、Silurana属、爪蟾属（Xenopus）以及外类群背尖鼻蟾（Rhinophrynus dorsalis）中采集了113个常染色体区域的编码序列，平均长度约300碱基对（范围：102–1695碱基对），同时还采集了线粒体基因组的一段序列。通过多种方法对这些数据进行分析后，本研究得到了((Xenopus, Silurana)(Pipa, Hymenochirus))拓扑结构的强力支持，且经地质校准的分化时间估算结果与多数化石的年代及系统发育亲缘关系估算值相符。

本研究结果为冈瓦纳大陆（Gondwanaland）裂解时期负子蟾科的生物地理格局与演化时序提供了新的认知，同时也印证了系统基因组数据或许是解决分子系统学中棘手问题的必要手段。