A fossil-calibrated time-tree of all Australian freshwater fishes

Australian freshwater fishes are a relatively species-poor assemblage, comprising a small number of Gondwanan lineages and a number of groups derived from repeated freshwater invasions by marine ancestors. In addition to being a comparatively small assemblage, they are both highly endemic and highly threatened. However, a comprehensive phylogeny for these taxa is lacking, which has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rate, and rates of trait evolution. Here, we present a comprehensive dated phylogeny of 412 Australian freshwater fishes. We include all formally recognized freshwater species plus a number of genetically distinct subpopulations, species awaiting formal description, and predominantly brackish-water species. The phylogeny was inferred using maximum-likelihood analysis of a multilocus data set comprising six mitochondrial and three nuclear genes from 326 taxa. We inferred the evolutionary timescale using penalized likelihood, then used a statistical approach to add 86 taxa for which no molecular data were available. The time-tree inferred in our study will provide a useful resource for macroecological studies of Australian freshwater fishes, by enabling corrections for phylogenetic non-independence in evolutionary and ecological comparative analyses.

澳大利亚淡水鱼类是一个物种相对贫乏的类群，由少量冈瓦纳（Gondwanan）支系以及多次由海洋祖先入侵淡水环境演化而来的类群构成。该类群不仅规模相对较小，同时兼具极高的特有性与极高的受威胁等级。然而目前仍缺乏针对这些类群的全面系统发育研究，这极大阻碍了对其系统发育多样性、灭绝风险分布、物种形成速率以及性状演化速率的相关研究。本研究构建了涵盖412种澳大利亚淡水鱼类的全面时间校准系统发育树（dated phylogeny），纳入了所有正式定名的淡水物种，以及多个遗传分化显著的亚种群、待正式描述的物种，还有多数以半咸水环境为主要栖息生境的类群。本研究通过对326个类群的6个线粒体基因（mitochondrial gene）与3个核基因（nuclear gene）组成的多位点数据集（multilocus data set）进行最大似然法（maximum-likelihood）分析，完成了初始系统发育树的推断；随后采用惩罚似然法（penalized likelihood）推断演化时间尺度，并通过统计方法补充了86个无分子数据的类群。本研究得到的时间树将为澳大利亚淡水鱼类的宏生态学（macroecological）研究提供宝贵的研究资源，可用于校正演化与生态比较分析中的系统发育非独立性（phylogenetic non-independence）问题。