A new method for integrating ecological niche modeling with phylogenetics to estimate ancestral distributions

Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package.

在旨在探究生物远古分布的进化生物学研究中，祖先分布范围估测（ancestral range estimation）及生态位模型（niche model）的古气候投影已成为常用手段。然而上述两类方法均存在互补性局限：祖先分布范围估测中对分布区的离散化刻画往往过于粗疏，尤其在短时间尺度下；而生态位模型投影则未纳入进化过程的考量。系统发育生态位建模（phylogenetic niche modeling）通过将进化关系信息整合至环境耐受特征的刻画中，可同时解决上述两类问题。我们提出了一种全新的系统发育生态位建模方法，该方法基于R语言开发实现。仅需输入古今气候数据、类群分布记录数据与经时间校准的系统发育树，本方法即可为每个现存类群构建生态位模型，通过祖先性状估测（ancestral character estimation）重建祖先生态位模型，并将这些模型投影至古气候数据集，从而推算某一演化支的历史地理分布范围。该方法既支持对系统发育树节点处的祖先分布范围进行估测，也可对演化支分支上的祖先分布范围进行推断。我们以一小群箭毒蛙科（Dendrobatidae）蛙类为研究对象验证了该方法，结果表明其可针对分布范围狭窄、分布记录稀缺的物种开展分布推断。此外我们通过模拟实验证实，本方法可在地理空间与环境空间中精准重建已知祖先的生态位特征。本方法以易用的软件包为载体，整合了生态位建模、系统发育学与祖先分布范围估测等多个跨领域研究方向。