Soni Vivak, Versoza Cyril J, Vallender Eric J, Jensen Jeffrey D, Pfeifer Susanne P
Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA.
Mol Biol Evol. 2025 Jun 4;42(6). doi: 10.1093/molbev/msaf119.
As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset (Callithrix jacchus) is of significance across multiple fields of research. However, at least 2 peculiarities of this species potentially preclude commonly utilized population genetic modeling and inference approaches: a high frequency of twin births and hematopoietic chimerism. We here investigate these effects within the context of demographic inference, demonstrating via simulation that neglecting these biological features results in significant mis-inference of the underlying population history. Based upon this result, we develop a novel approximate Bayesian inference approach accounting for both common twin births and chimeric sampling. In addition, we newly present population genomic data from 15 individuals sequenced to high coverage and utilize gene-level annotations to identify neutrally evolving intergenic regions appropriate for demographic inference. Applying our developed methodology, we estimate a well-fitting population history for this species, which suggests robust ancestral and current population sizes, as well as a size reduction roughly 7,000 years ago likely associated with a shift from arboreal to savanna vegetation in north-eastern Brazil during this period.
作为一种具有重要生物医学意义的物种，描述普通狨猴（Callithrix jacchus）的进化基因组学在多个研究领域都具有重要意义。然而，该物种至少有两个特性可能会妨碍常用的群体遗传建模和推断方法：双胞胎出生的高频率和造血嵌合体。我们在此研究人口推断背景下的这些影响，通过模拟表明忽略这些生物学特征会导致对潜在种群历史的重大错误推断。基于这一结果，我们开发了一种新的近似贝叶斯推断方法，该方法同时考虑了常见的双胞胎出生和嵌合体采样。此外，我们新展示了15个个体的高覆盖度测序群体基因组数据，并利用基因水平注释来识别适合人口推断的中性进化基因间区域。应用我们开发的方法，我们估计了该物种拟合良好的种群历史，这表明了强健的祖先和当前种群大小，以及大约7000年前的种群规模缩减，这可能与该时期巴西东北部从树木植被向热带稀树草原植被的转变有关。
