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（phylogenetic）关系推断是理解生物演化的关键组成部分。然而，当系统发育树存在短而古老的节间支、因祖先有效种群规模（ancestral effective population sizes）过大或祖先种群结构（ancestral population structure）导致普遍存在谱系冲突（genealogical discordance），以及趋同演化（homoplasy）频发时，准确的系统发育推断将极具挑战。
分歧时间（divergence time）推断同样受限于诸多因素：演化速率未知且不均一、化石记录（fossil record）不完整、化石与现生支系（extant lineages）间的关系存在不确定性，以及化石年代的估算误差。
理想情况下，可通过构建大型“系统发育基因组学（phylogenomic）”数据集，并采用适配演化过程特征的分析方法来克服上述挑战——这些特征包括谱系冲突、往复替换（recurrent substitution）、重组（recombination）、祖先种群结构、已采样与未采样类群间物种形成（speciation）后发生的基因流（gene flow），以及演化速率的异质性。
在部分系统发育研究问题中，可借助独立于化石的信息（如地质记录）来识别推测的多样化驱动因子，随后将其对应的估算分歧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（Pipidae）下的Pipa、Hymenochirus、Silurana与Xenopus四个属的多样化历史，便兼具诸多上述演化与分析层面的挑战。
这类蛙类的多样化事件发生于数千万年前，拥有相对丰富的化石记录，其分布跨越的大陆板块拥有被充分研究的古连通性地质记录，且不同研究中得到的演化亲缘关系估算结果存在显著分歧。
本研究借助高通量测序（high throughput sequencing）技术与公共数据库，构建了大型系统发育基因组学数据集，并采用多位点溯祖（multilocus coalescence）方法对演化亲缘关系进行推断。
我们从Pipa、Hymenochirus、Silurana、Xenopus以及外类群（outgroup taxon）Rhinophrynus dorsalis中，采集了113个常染色体（autosomal）编码区域的序列数据，其平均长度约为300碱基对（base pair）（范围：102~1695碱基对），同时还获取了部分线粒体基因组（mitochondrial genome）序列。
采用多种方法对上述数据进行分析后，得到了具有高支持度的((Xenopus, Silurana)(Pipa, Hymenochirus))拓扑结构（topology），且经地质校准（geologically calibrated）的分歧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一致。
本研究结果为冈瓦纳大陆（Gondwanaland）解体过程中负子蟾科类群多样化的生物地理学（biogeography）特征与年代学（chronology）框架提供了新认知，同时也证明了系统发育基因组学数据对于解决分子系统学（molecular systematics）中棘手问题的必要性。