Genetic linkage disequilibrium of deleterious mutations in threatened mammals.

IF 6.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Chunyan Hu, Gaoming Liu, Zhan Zhang, Qi Pan, Xiaoxiao Zhang, Weiqiang Liu, Zihao Li, Meng Li, Pingfen Zhu, Ting Ji, Paul A Garber, Xuming Zhou
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Abstract

The impact of negative selection against deleterious mutations in endangered species remains underexplored. Recent studies have measured mutation load by comparing the accumulation of deleterious mutations, however, this method is most effective when comparing within and between populations of phylogenetically closely related species. Here, we introduced new statistics, LDcor, and its standardized form nLDcor, which allows us to detect and compare global linkage disequilibrium of deleterious mutations across species using unphased genotypes. These statistics measure averaged pairwise standardized covariance and standardize mutation differences based on the standard deviation of alleles to reflect selection intensity. We then examined selection strength in the genomes of seven mammals. Tigers exhibited an over-dispersion of deleterious mutations, while gorillas, giant pandas, and golden snub-nosed monkeys displayed negative linkage disequilibrium. Furthermore, the distribution of deleterious mutations in threatened mammals did not reveal consistent trends. Our results indicate that these newly developed statistics could help us understand the genetic burden of threatened species.

受威胁哺乳动物中有害突变的遗传连锁不平衡。
在濒危物种中,针对有害突变的负选择所产生的影响仍未得到充分探索。最近的研究通过比较有害突变的积累来衡量突变负荷,然而,这种方法在比较系统发育上密切相关的物种种群内部和种群之间时最为有效。在这里,我们引入了新的统计量 LDcor 及其标准化形式 nLDcor,它允许我们使用无相位基因型检测和比较不同物种间有害突变的全球连锁不平衡。这些统计量测量平均的成对标准化协方差,并根据等位基因的标准差对突变差异进行标准化,以反映选择强度。我们随后研究了七种哺乳动物基因组的选择强度。老虎表现出有害突变的过度分散,而大猩猩、大熊猫和金丝猴则表现出负的连锁不平衡。此外,受威胁哺乳动物中有害突变的分布也没有显示出一致的趋势。我们的研究结果表明,这些新开发的统计数据可以帮助我们了解濒危物种的遗传负担。
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来源期刊
EMBO Reports
EMBO Reports 生物-生化与分子生物学
CiteScore
11.20
自引率
1.30%
发文量
267
审稿时长
1 months
期刊介绍: EMBO Reports is a scientific journal that specializes in publishing research articles in the fields of molecular biology, cell biology, and developmental biology. The journal is known for its commitment to publishing high-quality, impactful research that provides novel physiological and functional insights. These insights are expected to be supported by robust evidence, with independent lines of inquiry validating the findings. The journal's scope includes both long and short-format papers, catering to different types of research contributions. It values studies that: Communicate major findings: Articles that report significant discoveries or advancements in the understanding of biological processes at the molecular, cellular, and developmental levels. Confirm important findings: Research that validates or supports existing knowledge in the field, reinforcing the reliability of previous studies. Refute prominent claims: Studies that challenge or disprove widely accepted ideas or hypotheses in the biosciences, contributing to the correction and evolution of scientific understanding. Present null data: Papers that report negative results or findings that do not support a particular hypothesis, which are crucial for the scientific process as they help to refine or redirect research efforts. EMBO Reports is dedicated to maintaining high standards of scientific rigor and integrity, ensuring that the research it publishes contributes meaningfully to the advancement of knowledge in the life sciences. By covering a broad spectrum of topics and encouraging the publication of both positive and negative results, the journal plays a vital role in promoting a comprehensive and balanced view of scientific inquiry. 
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