Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes

The Andes are a major dispersal barrier for lowland rain forest plants and animals, yet hundreds of lowland tree species are distributed on both sides of the Northern Andes, raising questions about how the Andes influenced their biogeographic histories and population genetic structure. To explore these questions, we generated standardized datasets of thousands of SNPs from paired populations of 49 tree species co-distributed in rain forest tree communities located in Panama and Amazonian Ecuador and calculated genetic diversity (π) and absolute genetic divergence (dXY) within and between populations, respectively. We predicted (1) higher genetic diversity in the ancestral source region (east or west of the Andes) for each taxon, and (2) correlation of genetic statistics with species attributes, including elevational range and life-history strategy. We found that genetic diversity was higher in putative ancestral source regions, possibly reflecting founder events during colonization. We found little support for a relationship between genetic divergence and species attributes except that species with higher elevational range limits exhibited higher dXY, implying older divergence times. One possible explanation for this pattern is that dispersal through mountain passes declined in importance relative to dispersal via alternative lowland routes as the Andes experienced uplift. We found no difference in mean genetic diversity between populations in Central America and the Amazon. Overall, our results suggest that dispersal across the Andes has left enduring signatures in the genetic structure of widespread rain forest trees. We outline additional hypotheses to be tested with species-specific case studies.

Methods
The data consist of called genotypes of single nucleotide polymorphisms (SNPs) for 49 tropical rain forest tree species. Individuals were sampled from Yasuni, Ecuador and Barro Colorado Island (BCI), Panama, and sequenced using a double-digest Restriction-Associated DNA (ddRAD) approach. Data are presented as standard Variant Call Format (VCF) files.

安第斯山脉是低地雨林动植物的主要扩散屏障，然而仍有数百种低地树木物种在北安第斯山脉两侧均有分布，这引发了学界关于安第斯山脉如何影响其生物地理历史与种群遗传结构的疑问。为探究这些问题，我们针对分布于巴拿马与厄瓜多尔亚马逊地区的雨林树木群落中的49个共分布树木物种的配对种群，生成了包含数千个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的标准化数据集，并分别计算了种群内的遗传多样性（π）与种群间的绝对遗传分化（dXY）。我们提出两项预测：其一，每个类群的推定祖先起源区域（安第斯山脉东侧或西侧）具有更高的遗传多样性；其二，遗传统计指标与物种属性（包括海拔分布范围与生活史策略）存在相关性。

研究结果显示，推定的祖先起源区域的遗传多样性更高，这可能反映了定殖过程中的奠基者事件。除海拔分布范围上限更高的物种呈现出更高的dXY值（暗示其分化年代更为久远）外，我们几乎未发现遗传分化与物种属性之间存在关联的证据。针对这一模式的一种可能解释是：随着安第斯山脉隆升，经由山地隘口的扩散相较于通过其他低地路线的扩散，其重要性逐渐降低。我们未发现中美洲与亚马逊种群的平均遗传多样性存在显著差异。总体而言，本研究结果表明，跨安第斯山脉的扩散在广布雨林树木的遗传结构中留下了持久印记。我们还提出了可通过物种特异性案例研究加以验证的额外假说。

方法
本数据集包含49种热带雨林树木的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型基因型数据。样本采集自厄瓜多尔亚苏尼（Yasuni）与巴拿马巴罗科罗拉多岛（Barro Colorado Island, BCI），并采用双酶切限制性位点关联DNA（double-digest Restriction-Associated DNA, ddRAD）技术进行测序。数据以标准变异检测格式（Variant Call Format, VCF）文件形式提供。