Africa’s black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa’s Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.

中文翻译：

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种间基因流和黑白犀牛的专业化进化。

非洲的黑（Diceros bicornis）犀牛和白（Ceratotherium simum）犀牛是密切相关的姊妹类群，它们进化出高度分散的专性浏览和放牧喂养策略。尽管它们的前体物种Diceros praecox和Ceratotherium mauritanicum出现在化石记录中，约为5.2 Ma，但到4 Ma时，它们仍然是混合食性动物，甚至在时空上都同居于今天非洲裂谷的几个上新世遗址。在这里，我们问D. praecox和C. mauritanicum当它们进入上新世次生接触时被生殖隔离。我们测序并重新组装了第一个带注释的黑犀牛参考基因组，并将其与其他黑白犀牛的可用基因组进行了比较。我们显示祖传基因流之间的D. praecox和C. mauritanicum尽管采用常规方法从全基因组数据中检测基因流，但由于谱系分选不完全，返回了最近种间迁移的假阳性特征，所以在3.3 Ma和4.1 Ma之间的某个时间停止了检测。我们建议，在最初的分歧之后，正在进行的上新世遗传交换可能长达2 My，这可能会阻碍专性进食策略的发展，直到两个物种都被完全生殖分离为止，但是早更新世的更严重和变化的古气候可能是非洲犀牛生态专业化的最终推动者。