Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences

The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits.

We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits.

Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum.

Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.

群落组装(community assembly)相关过程的时序与速率，是群落生态学家与保护管理者高度关注的核心议题。化石记录是研究群落组成历史变化的宝贵数据来源，但往往分辨率不足，无法在区域或样地尺度上解析群落组装过程，同时追踪携带已知关联性状的已知物种种群的动态轨迹。

本研究提出了一套三步研究框架，用于解析物种随时间的现代积累过程：其一，对群落内多个物种种群的多个个体进行DNA采样；其二，利用分子定年(molecular dating)方法估算每个物种种群的溯祖时间(coalescence time)；其三，基于推断得到的种群年龄，绘制现代物种随时间的积累曲线。我们以澳大利亚东部三个雨林群落的植物全叶绿体基因组(chloroplast genome)数据为例，演示了该研究框架的应用。通过合并的高通量测序文库(high-throughput sequence library)，我们推断得到了每个群落内多个物种种群的预期溯祖时间，进而构建了每个群落的本地群落组装积累曲线。此外，我们还探讨了携带不同功能性状(functional trait)的物种种群，其群落组装积累曲线的差异特征。

平衡物种丰富度(equilibrium species richness)模型为我们的原假设(null hypothesis)提供了理论支撑，且在很大程度上解释了群落组装积累曲线的形态，同时表明群落物种积累过程的复杂性需要引入额外参数进行探究——例如设置具有不同灭绝速率(extinction rate)的物种种群类别。本研究样地的群落组装积累曲线显示，各个群落内均存在近期种群扩张的信号。这一近期物种积累的信号，与末次冰盛期(Last Glacial Maximum)之后适宜雨林生境的扩张相吻合。

我们构建群落组装积累曲线的方法，为物种积累数据的可视化提供了简洁可行的研究路径。该方法可用于验证相关假说，例如物种特异性生态属性的相对生存潜力。尽管本研究案例采用了源自全叶绿体测序的单核苷酸多态性(single-nucleotide polymorphism, SNP)数据，但该研究框架同样可应用于线粒体基因组(mitochondrial genome)以及其他类群的群落研究。