Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species - Data supporting published version

Invasive freshwater fish systems are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically-disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe x niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged approximately 140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly-discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

Methods
Full methods are contained within the methods section and supporting text of:

Blackwell et al. Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species.

入侵性淡水鱼类类群常可与本土同属物种发生杂交，进而导致独特且不可替代的遗传资源流失。本研究发现，2013至2016年新发现的、来自坦桑尼亚南部的科罗盖罗非鱼（Korogwe tilapia, *Oreochromis korogwe*）种群正面临与体型更大的入侵物种尼罗罗非鱼（Nile tilapia, *Oreochromis niloticus*）杂交的威胁。本研究结合形态学分析、微卫星等位基因频率检测与全基因组测序数据，证实坦桑尼亚南部湖泊（南巴瓦拉湖、鲁坦巴湖与米图帕湖）中的科罗盖罗非鱼种群，与坦桑尼亚北部地理隔离的种群（济吉河与姆林加诺水坝种群）存在显著分化。本研究同时在三处南部湖泊中发现了科罗盖罗非鱼与尼罗罗非鱼杂交个体的遗传学证据，并证实基因组内的基因渗入程度存在异质性。最后，本研究借助基因渗入程度最低的基因组区域，估算得出南北部科罗盖罗非鱼种群的分化时间约为14万年前，这表明南北种群的地理隔离并非近期人为移殖所致，且这些种群各自代表独立的进化显著单元。本研究最终得出结论：这些新发现且具有独特表型的慈鲷种群正面临与入侵物种杂交的威胁，并提出这些不可替代的遗传资源亟需开展保护干预措施。

材料与方法
完整的实验方法详见下述文献的方法章节与补充材料：
Blackwell等人. 新发现的慈鲷鱼类生物多样性正面临与外来物种杂交的威胁.