Data from: Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique

Background: Intraspecific genetic variation of African fauna has been signific
antly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Results: Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. Conclusions:
We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.

研究背景：非洲动物的种内遗传变异（intraspecific genetic variation）深受上新世-更新世（Plio-Pleistocene）时期剧烈气候波动的影响，但除大型哺乳动物外，针对稀树草原栖息动物的自然种群多样性的实证数据极为匮乏。贡氏假鳃鳉（Nothobranchius furzeri）是一种分布于非洲东南部的一年生鱼类，栖息于主河漫滩之外的零散临时稀树草原水塘中。该物种的扩散能力有限，影响其遗传结构的种群过程大概率同时作用于陆生与水生类群。贡氏假鳃鳉是衰老研究中的模式类群，多个已知地理起源的种群已被应用于实验室研究。本研究对分布范围内所有自然种群的贡氏假鳃鳉开展了遗传结构、多样性、历史种群动态及分化时间模式的分析。

研究结果：本研究结合线粒体（细胞色素b部分序列，长度687 bp）与核基因（13个微卫星）标记，对来自36个种群的693尾贡氏假鳃鳉进行了遗传结构与历史种群动态分析。遗传标记一致显示出显著的种群分化结构，并提示存在两个与流域相关的主要遗传类群。二者的分化时间可追溯至上新世（距今超过2百万年）。北部类群栖息于莫桑比克西南部与津巴布韦东部间断性谢富河（Chefu River）流域的稀树草原水塘中；南部类群（分布于莫桑比克最南部）可进一步划分，林波波河（Limpopo River）构成了其分化障碍（最大分化时间为1百万年）。强烈的生境破碎化（孤立的临时水塘）体现在即使相邻水塘间也存在显著的遗传结构，遗传漂变发挥了主要作用，且存在显著的距离隔离效应。历史种群动态分析显示，两个类群均处于持续扩张状态，分布边缘区域频繁出现奠基者效应，同时存在谢富河与林波波河种群间的二次接触证据。

研究结论：本研究证实了以下三点：（1）两个主要贡氏假鳃鳉支系间存在上新世前的古老分化，二者近期发生二次接触且未出现生殖隔离；（2）显著的遗传结构源于其生境的碎片化特征与距离隔离效应，表明该物种扩散能力有限、仅能进行短距离扩散，且扩散并非直接依赖河道路径；（3）林波波河可作为阻碍其扩散与基因交流的屏障。