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.

澳大利亚淡水鱼类组成相对物种贫乏，包括少量冈瓦纳起源的谱系以及多次由海洋祖先淡水入侵衍生的群体。除了构成相对较小的集合外，它们同时具有高度的特有性和高度受威胁的特性。然而，这些类群的全面系统发育树尚不存在，这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研究。在本研究中，我们呈现了412种澳大利亚淡水鱼类的全面定年系统发育树。我们包括了所有正式认可的淡水物种以及一些遗传上独特的亚种群、待正式描述的物种和以咸淡水为主的物种。该系统发育树是通过分析包含来自326个类群的六个线粒体和三个核基因的多位点数据集的最大似然分析推断得出的。我们利用惩罚似然法推断出进化时间尺度，然后采用统计方法为86个没有分子数据的类群添加了信息。本研究中推断出的时间树将为澳大利亚淡水鱼类的宏观生态学研究提供有价值的资源，通过在演化和生态比较分析中纠正系统发育非独立性，从而促进研究进程。