Data from: Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea

The family Melanotaeniidae (rainbowfishes) represents the largest monophyletic group of freshwater fishes found in Australia and New Guinea. The family consists of seven genera and a total of 81 species, which are broadly distributed throughout the region. We conducted a phylogenetic analysis of Melanotaeniidae based on nearly complete taxonomic sampling of all species. We sequenced seven protein coding mitochondrial genes and the first two introns of the nuclear S7 gene, for a total of 6827 base pairs. Our goal was to use the phylogeny to infer the biogeographic history of rainbowfishes in this region, to provide a framework for the timing of divergence within the family, and to test for possible introgression between species. We found strong support for the monophyly of Melanotaeniidae. Three species-poor genera-Cairnsichthys, Rhadinocentrus and Iriatherina-were all resolved as early branching lineages within the family. The three species-rich genera-Melanotaenia, Chilatherina and Glossolepis-did not form a single monophyletic group, but instead formed three monophyletic groups endemic to discrete geographic regions: western New Guinea, northern New Guinea, and southern New Guinea plus Australia, respectively. All three geographic regions also contained three to four additional lineages that were separated by large genetic divergences and were frequently sympatric (except in western New Guinea). Our molecular clock results provide much older estimates of divergence than some aspects of the present geological setting. For instance, the formation of the present day Central Highlands, the integration of the Birds Head region with the rest of New Guinea, and the present proximate position of Waigeo and Batanta islands relative to the Birds Head, are all younger than the rainbowfishes living there based on our molecular clock estimates. We also identified ten species that have likely experienced historical introgression. Most introgression events were between different groups within the northern New Guinea lineage and the Southern New Guinea/Australian lineages. Finally, we identified nearly 20 undescribed species within Melanotaeniidae, demonstrating that much work remains in describing freshwater fish diversity in this region.

虹银汉鱼科（Melanotaeniidae，俗称彩虹鱼）是分布于澳大利亚与新几内亚的最大淡水鱼类单系群。该科包含7个属，共计81个物种，广泛分布于该区域。
我们针对该科所有物种开展了近乎全覆盖的分类学采样，以此完成虹银汉鱼科的系统发育分析。我们测序了7个蛋白编码线粒体基因以及核S7基因的前两个内含子，总序列长度达6827个碱基对。
本研究旨在通过构建系统发育树推断该区域彩虹鱼的生物地理历史，为该科内物种分化时间提供分析框架，并检验物种间潜在的基因渐渗现象。
我们的分析强烈支持虹银汉鱼科的单系性。3个物种贫乏的属——凯恩斯银汉鱼属（Cairnsichthys）、细银汉鱼属（Rhadinocentrus）和艾瑞银汉鱼属（Iriatherina）——均被解析为该科内的早期分支类群。而3个物种丰富的属——虹银汉鱼属（Melanotaenia）、唇银汉鱼属（Chilatherina）和光泽银汉鱼属（Glossolepis）——并未形成单一单系群，而是分别形成了三个局限于特定地理区域的单系群：西新几内亚、北新几内亚，以及南新几内亚与澳大利亚。
这三个地理区域内还各包含3至4个遗传分化程度极高的演化支，且多数类群（西新几内亚区域除外）呈同域分布。
我们的分子钟分析结果显示，物种分化的时间早于当前部分地质环境的形成时间。例如，根据我们的分子钟估算，现今的中央高地形成、鸟头半岛区域与新几内亚其余区域的融合，以及卫吉岛（Waigeo）和巴丹塔岛（Batanta）相对于鸟头半岛的当前近距位置，均晚于栖息于此的彩虹鱼类群。
我们还鉴定出10个可能经历过历史基因渐渗的物种。多数渐渗事件发生于北新几内亚演化支内的不同类群，以及南新几内亚/澳大利亚演化支之间。
此外，我们在虹银汉鱼科内发现了近20个未被描述的物种，表明该区域的淡水鱼类多样性仍有大量类群有待发掘与描述。