Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome‐wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole‐genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange‐fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent–offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree‐ and SNP‐based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.

中文翻译：

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比较谱系、遗传和基因组相关性估计，为两种极度濒危鸟类的配对决策提供信息：对全球保护育种计划的影响。

许多高度濒危物种的保护管理策略包括保护育种，以防止灭绝和促进恢复。这些保护育种计划的配对决策可以根据谱系数据来确定，以最大限度地减少个体之间的相关性，从而避免近亲繁殖、最大限度地提高多样性并保持进化潜力。然而，当谱系浅薄或不完整时，保护育种计划很难使用这种方法。虽然遗传数据（即微卫星）可用于估计相关性以告知配对决策，但新出现的证据表明，这种方法在遗传上贫乏的物种中可能缺乏精度，并且可能从基因组数据（即数千个基因组）中获得更有效的估计。广泛的单核苷酸多态性（SNP）。在这里，我们使用全基因组重测序方法中的谱系、微卫星和 SNP，对新西兰特有的两种极度濒危鸟类：卡基/黑长脚鹬 ( Himantopus novaezelandiae ) 和 kākāriki karaka/橙额长尾小鹦鹉 ( Cyanoramphus ) 的相关性估计和随后的配对决策进行了比较马尔赫比）。我们的研究结果表明，在评估经验亲子关系和全兄弟姐妹关系时，SNP 比微卫星提供了更精确的相关性估计。此外，我们的结果表明，基于谱系的方法和基于 SNP 的方法之间的相关性估计和使用PMx 的后续配对建议最为相似。这些综合结果表明，SNP 可以代替强大的谱系，成为告知配对决策的有效工具，这对全世界许多谱系不佳的保护育种计划具有重要意义。