In times when herpesvirus genomic data were scarce, the cospeciation between these viruses and their hosts was considered to be common knowledge. However, as more herpesviral sequences were made available, tree reconciliation analyses started to reveal topological incongruences between host and viral phylogenies, indicating that other cophylogenetic events, such as intrahost speciation and host switching, likely played important roles along more than 200 million years of evolutionary history of these viruses. Tree reconciliations performed with undated phylogenies can identify topological differences, but offer insufficient information to reveal temporal incongruences between the divergence timing of host and viral species. In this study, we performed cophylogenetic analyses using time-resolved trees of herpesviruses and their hosts, based on careful molecular clock modelling. This approach enabled us to infer cophylogenetic events over time and also integrate information on host biogeography to better understand host–virus evolutionary history. Given the increasing amount of sequence data now available, mismatches between host and viral phylogenies have become more evident, and to account for such phylogenetic differences, host switches, intrahost speciations and losses were frequently found in all tree reconciliations. For all subfamilies in Herpesviridae, under all scenarios we explored, intrahost speciation and host switching were more frequent than cospeciation, which was shown to be a rare event, restricted to contexts where topological and temporal patterns of viral and host evolution were in strict agreement.

中文翻译：

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宿主内物种和宿主转换在疱疹病毒的进化中发挥重要作用


在疱疹病毒基因组数据稀缺的时代，这些病毒与其宿主之间的共生被认为是常识。然而，随着更多的疱疹病毒序列可用，树协调分析开始揭示宿主和病毒系统发育之间的拓扑不一致，这表明其他共系统发育事件，例如宿主内物种形成和宿主转换，可能在超过 2 亿年的进化过程中发挥了重要作用。这些病毒的历史。使用未注明日期的系统发育进行的树协调可以识别拓扑差异，但提供的信息不足以揭示宿主和病毒物种的分歧时间之间的时间不一致。在这项研究中，我们基于仔细的分子钟建模，使用疱疹病毒及其宿主的时间分辨树进行了共系统发育分析。这种方法使我们能够推断随时间变化的共系统发育事件，并整合宿主生物地理学信息，以更好地了解宿主-病毒进化历史。鉴于现在可用的序列数据量不断增加，宿主和病毒系统发育之间的不匹配变得更加明显，并且为了解释这种系统发育差异，在所有树协调中经常发现宿主转换、宿主内物种形成和丢失。对于疱疹病毒科的所有亚科，在我们探索的所有情况下，宿主内物种形成和宿主转换比共物种更频繁，后者被证明是一种罕见事件，仅限于病毒和宿主进化的拓扑和时间模式严格一致的环境。