Most species are extinct; those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression and admixture, are therefore likely to involve “ghosts”, i.e. extinct, unknown or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario.

中文翻译：

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幽灵谱系极大地影响渗入测试的解释


大多数物种已经灭绝；那些不存在的通常是未知的。测序和采样的物种通常是已知物种的少数。因此，过去涉及水平基因流动的进化事件，例如水平基因转移、杂交、基因渗入和混合，很可能涉及“幽灵”，即灭绝的、未知的或未取样的谱系。这些幽灵谱系的存在已被广泛承认，但它们对基因流检测和所涉及物种识别可能产生的影响却在很大程度上被忽视了。它通常被认为是一个可能的误差源，通过合理的近似，可以忽略它。我们通过量化流行的 D 统计方法检测到的幽灵谱系对基因渗入的影响，探讨了缺失物种对进化研究的可能影响。我们从模拟数据中发现，在某些经常遇到的条件下，如果不考虑幽灵谱系，水平基因流的供体和受体可能会被错误地识别。特别是，通常推荐的远距离外群体会导致错误概率增加，并在大多数情况下导致错误解释。我们的结论是，幽灵谱系的基因渗入应该被系统地考虑为另一种可能的、甚至可能的情况。