对比全基因组和减少表示序列为人口人口统计和适应性推断:阿尔卑斯山哺乳动物的案例研究
Daria Martchenko1, Aaron B A Shafer2,3
1Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada. dariamartchenko@trentu.ca.
Heredity
|August 2, 2023
概括
整个基因组和减少表示序列测序都显示了北美山山羊的冰川替代性和低有效种群规模. 整个基因组测序为推断适应过程和同胞性运行提供了优势.
科学领域:
- 人口基因组学是人口的基因组学.
- 保护遗传学 保护遗传学
- 野生动物生物学 野生动物生物学
背景情况:
- 基因组数据捕获物种的进化历史,但测序策略和样本大小影响推断.
- 了解种群结构和适应潜力对于保护至关重要,尤其是面临环境变化的物种.
研究的目的:
- 为了比较全基因组再测序 (WGS) 和限制部位相关的DNA测序 (RADseq),以推断北美山羊 (Oreamnos americanus) 的人口和适应信号.
- 评估地理和气候对遗传多样性的影响,并评估物种在预测的环境变化下适应能力.
主要方法:
- 应用RADseq对254个个体和WGS对35个个体 (9X覆盖率) 和5个个体 (30X覆盖率) 在整个物种的范围.
- 使用ANGSD进行基因型概率,以及 δaδi和MSMC2进行人口建模.
- 使用冗余分析来评估遗传多样性的气候和地理预测因素.
主要成果:
- 无论是WGS还是RADseq的数据都始终支持冰川牧羊和山山山羊的极低有效种群规模 (Ne).
- 地理和气候变量解释了基因多样性的适度比例 (WGS为36%,RADseq为21%).
- 这两种方法都表明了遗传漂移和一些本地适应的重大影响,WGS为适应过程提供了更丰富的见解.
结论:
- WGS和RADseq都有效地检测大规模的人口和适应信号,尽管WGS在某些分析中提供了更高的分辨率.
- 北美山羊的遗传多样性很低,由于预测气候变化对高山环境的影响,它面临着可疑的长期适应能力.
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