Genus-wide paleogenetic analysis of Middle to Late Pleistocene extinct straight-tusked elephants (Palaeoloxodon) to infer phylogeography and patterns of admixture

大部分不为人知的灭绝的直齿象（古齿象）曾经在非洲和欧亚大陆的广大地区漫游。象属是象科的一部分，象科还包括三种现存的大象。古齿龙标本已被证明具有挑战性的位置在系统发育树使用形态学特征。此外，它们还显示出使古成因（=古DNA = aDNA）研究复杂化的特征，即分布在温暖的气候和相对较高的年龄，这两者都不利于DNA的保存。然而，为数不多的研究揭示了令人惊讶的结果，严重改变了我们对象科进化的看法。生成的DNA序列是来自非永久冻土地区的一些最古老的DNA序列，表明古齿龙在系统发育树上属于一个不同的分支，而不是之前认为的那样。单一可用的高覆盖率基因组显示，这个古齿象标本与象科中两个不同的谱系表现出高度的混合。显然，需要更多的数据，扩大目前样本的地理范围（四个来自德国，一个来自意大利），以及获得的信息深度。拟议的研究将产生第一个全属范围内的古成因概述，确定物种的数量和分布。对更新世的分化时间、种群规模变化和混合事件的估计使我们有机会将这些事件与气候周期联系起来，帮助我们理解气候变化与物种反应之间的联系。

The largely unknown extinct straight-tusked elephants (Palaeoloxodon) once roamed wide parts of Africa and Eurasia. The genus is part of the family Elephantidae, which also encompasses the three living elephant species. Palaeoloxodon specimens have been proven challenging to place in the phylogenetic tree using morphological features. Additionally, they display features complicating paleogenetic (= ancient DNA = aDNA) research, namely a distribution in warm climates and a relatively high age, which both are detrimental for DNA preservation. However, the few studies carried out revealed surprising results, severely altering our view of the evolution of Elephantidae. The DNA sequences generated, which are some of the oldest from non-permafrost regions, showed that Palaeoloxodon belonged to a different branch in the phylogenetic tree than previously believed. The single available high-coverage genome revealed that this Palaeoloxodon specimen showed high levels of admixture with two different lineages within the Elephantidae. Clearly, more data is needed, extending the geographical range of the current samples (four from Germany and one from Italy) and also the depth of information obtained. The proposed research will generate the first genus-wide paleogenetic overview over Palaeoloxodon, determining the number and distribution of species. Estimations of divergence times, population size changes, and events of admixture during the Pleistocene hold the opportunity to link these events to climatic cycles, helping our understanding of the connection between climate change and species reactions.