Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole ( Anolis carolinensis ) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retro...

转座因子（transposable elements, TEs）与其宿主之间的互作，是自然界中已知最具深远影响的协同进化过程之一。TEs的种群动态取决于各TE家族特有的多项因素，例如转座速率与插入偏好性、宿主的种群历史以及基因组格局。这些因素之间的交互机制尚未得到全面探究。本研究以绿安乐蜥（*Anolis carolinensis*，卡罗莱纳安乐蜥）为研究对象，其基因组中蕴含极为多样的TE类群，涵盖非长末端重复序列逆转座子（non-LTR retrotransposons）、短散在重复序列（SINEs）、长末端重复序列逆转座子（LTR-retrotransposons）与DNA转座子（DNA transposons）。我们观察到，对于长散在重复序列（LINEs）、短散在重复序列（SINEs）及DNA转座子，重组速率与TEs的频率及密度呈显著正相关。针对上述元件，种群历史对TE的频率与丰度存在明确影响：在近期扩张的种群中，多态性TE元件发生丢失且频率谱呈现偏倚。另一方面，部分长末端重复序列逆转座子...