Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell

Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable. Here, we use ancient DNA (aDNA) extracted from fossil eggshell, together with target enrichment and next-generation sequencing techniques, to reconstruct an additional new mitogenome from Aepyornis sp. with 33.5X coverage. We also recover the first elephant bird nuclear aDNA, represented by 12,500 bp of exonic information. While we confirm that elephant birds are sister taxa to the kiwi, our data suggests that, like neognaths, palaeognaths underwent an explosive radiation between 69-52 Ma—well after the break-up of Gondwana, and more rapidly than previously estimated from mitochondrial data alone. These results further support the idea that ratites primarily diversified immediately following the Cretaceous-Palaeogene mass extinction and convergently evolved flightlessness. Our study reinforces the importance of including information from the nuclear genome of extinct taxa for recovering deep evolutionary relationships. Furthermore, with approximately 3% endogenous aDNA retrieved, avian eggshell can be a valuable substrate for recovering high quality aDNA. We suggest that elephant bird whole genome recovery is ultimately achievable, and will provide future insights into the evolution these birds.古颚总目（Palaeognaths）是所有现生鸟类其余类群——新颚类（neognaths）——的姊妹群，曾被认为是冈瓦纳超大陆解体后遗留的地理隔离孑遗类群。然而近期的分子研究却提出，会飞的古颚类祖先曾跨越海洋屏障进行扩散。解决这一学术争议的核心，在于准确重建其演化关系并测定分化时间，而这往往依赖于已灭绝近亲的系统发育信息与核基因组数据。此前来自马达加斯加已灭绝象鸟的线粒体基因组（mitogenomes）曾为古颚类系统发育研究提供了参考，但核基因组信息始终未能获取。本研究利用从化石蛋壳中提取的古DNA（ancient DNA，aDNA），结合目标富集与下一代测序技术，成功重建了覆盖度达33.5倍的未定种象鸟（Aepyornis sp.）全新线粒体基因组。同时，我们首次获取了象鸟的核古DNA序列，包含12500 bp的外显子区域信息。研究确认象鸟与几维鸟（kiwi）互为姊妹群，但数据表明，与新颚类一样，古颚类在6900万至5200万年前经历了爆发式辐射演化——这一时间远晚于冈瓦纳超大陆的解体，且演化速率较此前仅基于线粒体数据的估算更快。上述结果进一步支持了"平胸鸟类（ratites）主要在白垩纪-古近纪大灭绝后迅速分化，并独立演化出飞行能力丧失特征"的观点。本研究凸显了纳入已灭绝类群核基因组信息对于解析深层演化关系的重要性。此外，本次研究成功获取了约3%的内源性古DNA，证明鸟类蛋壳是获取高质量古DNA的优质载体。我们认为，象鸟全基因组的最终获取是可行的，这将为后续深入解析这类鸟类的演化历程提供关键见解。