Department of Genetics, Genomics & Cancer Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
Current address: Faculty of Science & Engineering, Swansea University, Swansea, UK.
BMC Ecol Evol. 2024 Oct 31;24(1):134. doi: 10.1186/s12862-024-02324-0.
Great apes are a global conservation concern, with anthropogenic pressures threatening their survival. Genetic analysis can be used to assess the effects of reduced population sizes and the effectiveness of conservation measures. In humans, autosomal short tandem repeats (aSTRs) are widely used in population genetics and for forensic individual identification and kinship testing. Traditionally, genotyping is length-based via capillary electrophoresis (CE), but there is an increasing move to direct analysis by massively parallel sequencing (MPS). An example is the ForenSeq DNA Signature Prep Kit, which amplifies multiple loci including 27 aSTRs, prior to sequencing via Illumina technology. Here we assess the applicability of this human-based kit in African great apes. We ask whether cross-species genotyping of the orthologs of these loci can provide both individual and (sub)species identification.
The ForenSeq kit was used to amplify and sequence aSTRs in 52 individuals (14 chimpanzees; 4 bonobos; 16 western lowland, 6 eastern lowland, and 12 mountain gorillas). The orthologs of 24/27 human aSTRs amplified across species, and a core set of thirteen loci could be genotyped in all individuals. Genotypes were individually and (sub)species identifying. Both allelic diversity and the power to discriminate (sub)species were greater when considering STR sequences rather than allele lengths. Comparing human and African great-ape STR sequences with an orangutan outgroup showed general conservation of repeat types and allele size ranges. Variation in repeat array structures and a weak relationship with the known phylogeny suggests stochastic origins of mutations giving rise to diverse imperfect repeat arrays. Interruptions within long repeat arrays in African great apes do not appear to reduce allelic diversity.
Orthologs of most human aSTRs in the ForenSeq DNA Signature Prep Kit can be analysed in African great apes. Primer redesign would reduce observed variability in amplification across some loci. MPS of the orthologs of human loci provides better resolution for both individual and (sub)species identification in great apes than standard CE-based approaches, and has the further advantage that there is no need to limit the number and size ranges of analysed loci.
大型猿类是全球关注的保护对象，人为压力威胁着它们的生存。遗传分析可用于评估种群规模缩小的影响以及保护措施的有效性。在人类中，常染色体短串联重复序列（aSTR）广泛用于群体遗传学以及法医个体识别和亲属关系测试。传统上，通过毛细管电泳（CE）进行基于片段长度的基因分型，但越来越倾向于通过大规模平行测序（MPS）进行直接分析。例如，ForenSeq DNA Signature Prep Kit 可扩增包括 27 个 aSTR 在内的多个基因座，然后通过 Illumina 技术进行测序。在此，我们评估了这种基于人类的试剂盒在非洲大型猿类中的适用性。我们询问这些基因座的同源物的跨物种基因分型是否可以提供个体和（亚种）识别。
ForenSeq 试剂盒用于扩增和测序 52 个个体（14 只黑猩猩；4 只倭黑猩猩；16 只西部低地大猩猩、6 只东部低地大猩猩和 12 只山地大猩猩）的 aSTR。27 个人类 aSTR 中的 24 个同源物在物种间扩增，所有个体都可以对 13 个核心基因座进行基因分型。基因型可以个体和（亚种）识别。当考虑 STR 序列而不是等位基因长度时，等位基因多样性和区分（亚种）的能力更大。将人类和非洲大型猿类的 STR 序列与一个猩猩外群进行比较表明，重复类型和等位基因大小范围普遍保守。重复数组结构的变异以及与已知系统发育的弱关系表明，突变的起源是随机的，导致不同的不完美重复数组。非洲大型猿类中长重复数组的中断似乎不会降低等位基因多样性。
ForenSeq DNA Signature Prep Kit 中的大多数人类 aSTR 的同源物可以在非洲大型猿类中进行分析。引物重新设计将减少一些基因座中观察到的扩增变异性。人类基因座同源物的 MPS 为大型猿类的个体和（亚种）识别提供了比标准 CE 方法更好的分辨率，并且具有进一步的优势，即无需限制分析基因座的数量和大小范围。
