Data from: A comparison of pedigree- and genetic-based measures for identifying inbreeding depression in the critically endangered Attwater’s Prairie-chicken

The primary goal of captive breeding programs for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study both pedigree- and DNA-based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie-chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction of neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree-based inbreeding coefficients (f_pedigree) was less than that obtained from DNA-based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree-based measures when controlling for additional variables such as age, breeding facility, gender, and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie-chickens. This study highlights the importance of using DNA-based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.濒危物种圈养繁殖计划（captive breeding programs）的核心目标为防止物种灭绝，而保护遗传多样性（genetic diversity）、规避近交（inbreeding）正是该目标的重要组成部分。此类计划通常通过最小化种群内的平均亲缘关系（mean kinship），以维持用于建立圈养种群的遗传奠基者（genetic founders）的遗传贡献均等。若谱系（pedigree）存在错误，该方法在缓解近交衰退（inbreeding depression）方面的有效性便会降低。本研究同时采用谱系分析法（pedigree-based methods）与DNA分析法（DNA-based methods），评估极危物种阿特沃特草原榛鸡（Tympanuchus cupido attwateri）的圈养种群是否存在近交衰退。该物种为草原松鸡的一个亚种，其种群数量已出现显著下降，同时中性遗传多样性（neutral genetic diversity）亦随之降低。在检测圈养种群的近交迹象时，基于谱系计算的近交系数（inbreeding coefficients, f_pedigree）的变异程度低于基于DNA分析得到的近交系数（f_DNA）。圈养环境下雏鸟与成体的死亡率，分别与亲本亲缘关系（parental relatedness, r_DNA）及f_DNA呈显著正相关；而在控制年龄、繁殖设施、性别以及圈养/放归状态等额外变量后，基于谱系的相关指标并未展现出此类相关性。此外，个体位点纯合度（individual homozygosity by loci, HL）与亲本r_DNA值，分别与圈养成体死亡率及雏鸟致死性先天性缺陷（lethal congenital defect）的发生呈正相关，这表明近交可能是提升阿特沃特草原榛鸡此类病症发生频率的一个影响因素。本研究凸显了在谱系不完整，或因配对信息不确定导致谱系存在误差时，采用DNA分析法为管理决策提供更科学依据的重要性。