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Conservation genetics: 50 Years and counting
Conservation Letters ( IF 8.5 ) Pub Date : 2020-12-30 , DOI: 10.1111/conl.12789
Cock van Oosterhout 1
Affiliation  

It has been 50 years since the landmark paper by Frankel highlighted the importance of genetic variation for continued evolution in the conservation of species. Despite major technological and theoretical advances in the analysis of genome data, we have failed to fully integrate genetics into conservation practice. The IUCN does not incorporate genetic data into their Red List assessment of species, and the relatedness of individuals in the studbooks of zoos are still only assessed by using pedigree records that contain uncertainty and error. Several obstacles have been responsible for the slow uptake of genetics in conservation: (1) the primary objectives of our activities differ across the conservation community; (2) inequality in exposure to advanced sequencing technologies and analytical tools has created a communication gap; and (3) most money in research has been allocated to funding scientific advances rather than their applications in the real world. These obstacles are more important than other alleged problems, such as the costs or complexity of genetic analyses, or scepticism about the relevance of genetic variation in species conservation. Fortunately, once acknowledged, these obstacles can be redressed so that real progress can be made in conservation.

Conservation biology is a “mission‐oriented crisis discipline” that aims to evaluate human impacts on biodiversity and prevent the extinction of species. It is a multidisciplinary approach that integrates theories from the fields of ecology, ethology, demography, taxonomy, and genetics. The insights gained from these disciplines underpin many management decisions taken by conservation practitioners. Crucially, however, two parties in the conservation community—that is, the “geneticists” and the “practitioners on the ground”—have prioritized different outcomes. The latter group consists of NGO conservation professionals—supported in various degrees by local government bureaucrats—and they have been working tirelessly on saving species from extinction by stopping habitat loss and/or mitigating its consequences. On the other hand, the geneticists and bioinformaticians have been improving their methods to quantify genetic variation and assess the mutation load in populations, developing evermore integrated and advanced analyses. These scientific endeavors have been fuelled by the funding environment in academia, which tends to evaluate the quality of research by the number of papers published in high impact journals, the number of citations, and patents. Less value has been given to the actual impact of the research on real‐world problems, such as saving a species from extinction. Although this is gradually changing, this long‐standing difference in values has further increased the divide between both parties. The drive for advancing technology and methods also meant that the understanding of the analyses has moved even further out of reach of nonexperts. Indeed, in this fast‐moving field, methods became obsolete even before they could be learned or applied in practical conservation. Sadly, our quest for increasingly advanced analytical tools may have steered us further away from what should have always been our primary objective—saving species from extinction and protecting their habitats. Do we really need a handheld sequencing machine to conduct meaningful conservation work? Rather than a Star‐Trek‐like tricorder, what the conservation community really needs are some nails and hammers to save the rocking ship from sinking.

For conservation genetics, the past 50 years have shown that “the perfect is the enemy of the good.” Yes, we have come a far way, and what can be done now with genomics we could not have imagined 50 years ago. However, the biggest advance we can make now is to stop tinkering with our tools. We must decide on a standardized set of summary statistics that can be extracted from genome data in a routine fashion. Those statistics need to be simple so that they can be understood by the whole conservation community. The statistics need to assess the severity of genomic erosion that impairs the fitness of individuals and the viability of populations: (1) the loss of genetic variation due to inbreeding and drift; (2) the introgression of genomes by the hybridization of species (rather than admixture); and (3) the accumulation and expression of deleterious mutations. So much can be learned by analyzing the genome of just a single individual of a population or species. It captures the signatures of past selection and the demographic history of an entire species, dating back to events from far before the current population decline. Those past events are important because the potential scars they may have left in the genome will affect the future viability of populations and species. Hence, these data are critical to help direct conservation management.

Furthermore, the statistics will need to conform to a universal standard to ensure that they are comparable across (closely related) species. The development of a "gold standard" approach is already underway for genome sequencing; the conservation genetic community now will need to adopt a similar approach for the downstream analyses. Once a set of robust statistics has been decided, they can be included in the IUCN Red List assessment as an addendum for each species. With the Earth BioGenome Project and many whole‐genome sequencing projects underway, genomic data are rapidly being generated for many species. Conservation biologists can now post samples of their species to these sequencing consortiums to obtain high‐quality reference genomes. The next step is to develop a service that can perform the downstream analyses to calculate and report these genomic summary statistics in an internationally accepted universal standard. I believe the insights gleaned from these statistics will significantly enhance conservation practice. First, they will improve the assessment of the long‐term extinction risks of species in the Red List, highlighting trends across taxonomies that may have thus far gone unnoticed. Although this may not be of immediate use to conservation on the ground, it could help to inform wider conservation policies and strategies relevant to the 2030 Agenda for Sustainable Development of the United Nations. Second, those statistics can also be calculated for a larger number of individuals of a species or population in resequencing projects. Such data are valuable for conservation on the ground, for example to assess the impact of different management strategies, and to inform ex situ conservation and genetic rescue programs.

Conservation practitioners have applied crucial “first aid,” saving many threatened species from imminent extinction. It is now time to provide “second aid” to ensure that the small populations continue to thrive. This requires the integration of population genetic theory and genomic know‐how into conservation; this must be done now, rather than pondering for another 50 years.



中文翻译:

保护遗传学:50年和计数

自弗兰克尔(Frankel)具有里程碑意义的论文强调遗传变异对于物种保护的持续进化的重要性以来已有50年了。尽管在基因组数据分析方面取得了重大技术和理论上的进步,但我们仍未能将遗传学完全纳入保护实践。IUCN并未将遗传数据纳入其物种的红色名录评估中,并且仍仅通过使用包含不确定性和错误的谱系记录来评估动物园梭哈簿中个体的相关性。保护方面遗传学的缓慢吸收造成了以下障碍:(1)我们的活动的主要目标在保护社区中有所不同;(2)接触先进测序技术和分析工具的不平等造成了沟通鸿沟;(3)研究中的大部分资金已分配给科学进步,而不是其在现实世界中的应用。这些障碍比其他所谓的问题更为重要,例如遗传分析的成本或复杂性,或者对物种保护中遗传变异的相关性持怀疑态度。幸运的是,一旦认识到这些障碍,就可以纠正这些障碍,从而在保护方面取得真正的进展。

保护生物学是一门“任务导向的危机学科”,旨在评估人类对生物多样性的影响并防止物种灭绝。它是一种多学科方法,将生态学,人类学,人口统计学,分类学和遗传学等领域的理论融合在一起。从这些学科中获得的见识支持了保护从业人员做出的许多管理决策。然而,至关重要的是,保护界中的两个当事方,即“遗传学家”和“实地执业者”,已将不同的结果列为优先事项。后者由NGO保护专业人员组成,并得到了当地政府官员的不同程度的支持,他们一直在不懈地努力,通过阻止栖息地的丧失和/或减轻其后果来保护物种免遭灭绝。另一方面,遗传学家和生物信息学家一直在改进他们的方法,以量化遗传变异并评估种群中的突变负荷,从而发展出越来越先进的综合分析方法。学术界的资助环境助长了这些科学的努力,学术界倾向于通过在高影响力期刊上发表的论文数量,引文数量和专利来评估研究的质量。该研究对现实世界问题的实际影响的价值较低,例如使物种免于灭绝。尽管这种情况正在逐渐改变,但这种长期的价值观差异进一步扩大了双方之间的鸿沟。推动技术和方法发展的动力还意味着,对分析的理解已经远远超出了非专家的能力范围。确实,在这个飞速发展的领域,方法甚至在被学习或应用于实际保护之前就已经过时了。令人遗憾的是,我们对日益先进的分析工具的追求可能使我们偏离了原本应该成为我们主要目标的目标,即使物种免于灭绝并保护其栖息地。我们真的需要手持式测序仪来进行有意义的保护工作吗?保护社区真正需要的不是钉钉锤三叉戟,而是一些钉子和锤子,以保护摇摆船免于下沉。我们对日益先进的分析工具的追求可能使我们远离本应始终是我们的主要目标的目标,即使物种免于灭绝并保护其栖息地。我们真的需要手持式测序仪来进行有意义的保护工作吗?保护社区真正需要的不是钉子一样的三叉戟,而是一些钉子和锤子,以保护摇摆的船免于下沉。我们对日益先进的分析工具的追求可能使我们远离本应始终是我们的主要目标的目标,即使物种免于灭绝并保护其栖息地。我们真的需要手持式测序仪来进行有意义的保护工作吗?保护社区真正需要的不是钉子一样的三叉戟,而是一些钉子和锤子,以保护摇摆的船免于下沉。

对于保护遗传学而言,过去50年表明“完美是善良的敌人”。是的,我们已经走了很长一段路,现在用50年前无法想像的基因组学可以做什么。但是,我们现在可以取得的最大进步就是停止修补我们的工具。我们必须决定可以以常规方式从基因组数据中提取的一组标准化的摘要统计信息。这些统计数据必须很简单,以便整个保护界都能理解。统计数据需要评估损害个体适应性和种群生存能力的基因组侵蚀的严重程度:(1)近交和漂移造成的遗传变异损失;(2)通过种的杂交(而不是混合)使基因组渗入;(3)有害突变的积累和表达。通过仅分析种群或物种中单个个体的基因组,可以学到很多东西。它捕获了过去选择的特征以及整个物种的人口历史,其历史可以追溯到当前种群下降之前的很长时间。这些过去的事件很重要,因为它们可能遗留在基因组中的潜在疤痕将影响种群和物种的未来生存能力。因此,这些数据对于帮助指导保护管理至关重要。

此外,统计数据将需要符合通用标准,以确保它们在(密切相关的)物种中具有可比性。基因组测序的“金标准”方法已经在开发中。现在,保护遗传界将需要采取类似的方法进行下游分析。一旦确定了一套可靠的统计数据,就可以将它们作为每个物种的附录列入IUCN红色名录评估。随着地球生物基因组计划和许多全基因组测序计划的进行,正在为许多物种快速生成基因组数据。保护生物学家现在可以将其物种的样本发布到这些测序联盟中,以获得高质量的参考基因组。下一步是开发一种服务,该服务可以执行下游分析,以国际公认的通用标准计算和报告这些基因组摘要统计数据。我相信从这些统计数据中收集到的见解将大大增强保护实践。首先,他们将改善对《红色名录》中物种长期灭绝风险的评估,突出显示迄今为止尚未引起人们注意的生物分类学趋势。尽管这可能不适用于实地的保护,但它可能有助于为与联合国《 2030年可持续发展议程》有关的更广泛的保护政策和战略提供信息。其次,在重新排序项目时,也可以为一个物种或种群中的更多个体计算这些统计数据。

养护从业人员已经应用了至关重要的“急救”措施,使许多濒临灭绝的物种免于濒临灭绝。现在该提供“第二援助”,以确保少数群体继续蓬勃发展。这就需要将种群遗传学理论和基因组专门知识整合到保护中。现在必须这样做,而不是再考虑50年。

更新日期:2020-12-30
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