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）是澳大利亚与新几内亚地区现存规模最大的单系淡水鱼类类群（monophyletic group）。该科涵盖7个属，总计81个物种，广泛分布于该区域范围内。本研究基于所有物种的近乎完整分类学采样，开展了虹银汉鱼科的系统发育分析（phylogenetic analysis）：我们测序了7个蛋白编码线粒体基因以及核基因S7的前两个内含子序列，拼接序列总长度达6827个碱基对（base pair）。

本研究的目标在于：借助构建的系统发育树推断该区域彩虹鱼的生物地理历史（biogeographic history），为该科内物种分化时间提供研究框架，并检验物种间可能存在的基因渐渗（introgression）现象。

研究结果显示，本研究的系统发育分析强烈支持虹银汉鱼科的单系性。三个物种稀少的属——Cairnsichthys、Rhadinocentrus与Iriatherina——均被解析为该科内早期分化的支系（lineage）。而三个物种丰富的属：Melanotaenia、Chilatherina与Glossolepis并未形成单一单系群，而是分别构成了三个为特定地理区域所特有的单系支系：依次为新几内亚西部、新几内亚北部，以及新几内亚南部与澳大利亚。

三个地理区域内还各包含3至4个遗传分化程度极高的支系，且除新几内亚西部外，其余区域的多数支系均为同域分布（sympatric）。我们的分子钟（molecular clock）估算结果显示，物种分化时间早于当前部分地质环境的形成时间。例如，现今中央高地的形成、鸟头半岛与新几内亚其余区域的融合，以及卫吉岛（Waigeo）与巴丹塔岛（Batanta）相对于鸟头半岛的当前邻近位置，均晚于我们基于分子钟估算的当地栖息彩虹鱼的分化时间。

本研究还鉴定出10个大概率经历过历史基因渐渗的物种，多数渐渗事件发生在新几内亚北部支系内的不同类群，以及新几内亚南部/澳大利亚支系之间。最后，我们在虹银汉鱼科内发现了近20个未被描述的物种，这表明该区域淡水鱼类多样性的分类学研究仍有大量工作亟待完成。