Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA, 93105, USA.
Research and Collections, Department of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA, 90007, USA.
BMC Ecol Evol. 2022 Mar 2;22(1):22. doi: 10.1186/s12862-022-01981-3.
Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones.
Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray-Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones.
The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.
拟鲿属（Hypseleotris）鱼类是澳大利亚淡水鱼类区系的重要组成部分，其物种分布于该大陆的西部、北部和东部。我们基于核超保守元素（UCE）序列，使用贝叶斯估计分歧时间来推断该属的校准系统发育，并使用该系统发育通过 GeoSSE 来研究地理多样化模式。东南部的物种已经发生杂交，形成了半克隆谱系，我们还解决了半克隆谱系的关系，并将其在 UCE 系统发育中的系统发育位置与基于完整线粒体基因组的假设进行了比较。然后，我们使用从 UCE 序列中提取的分相 SNPs 对东南部物种和半克隆谱系进行种群结构分析。
分布广泛的广盐性物种 Hypseleotris cyprinoides 从整个印度洋-太平洋地区都有记录，其结果在其余物种之外。澳大利亚的两个辐射区构成了 Hypseleotris 的大部分，一个主要分布在西北部沿海河流，另一个分布在东南部地区，包括墨累-达令、布卢-班卡尼亚和艾尔湖流域，以及大分水岭以东的沿海河流。我们的系统发育结果显示 UCE 和线粒体假设之间存在核质不符，将半克隆杂交种置于其亲代类群之间，并表明 Kimberleyeleotris 属嵌套在西北部 Hypseleotris 辐射区内，还有三个未描述的物种。我们推断 Hypseleotris 的冠层年龄为 17.3Ma，澳大利亚物种的辐射时间约为 10.1Ma，西北部（不包括 H. compressa）和东南部辐射的冠层年龄分别为 5.9 和 7.2Ma。使用 GeoSSE 的基于范围的多样化分析表明，西北和东南澳大利亚辐射区以及 Kimberley 地区和 Arnhem 高原较小的物种辐射区之间的物种形成和灭绝率一直保持稳定。分相 SNPs 的分析证实了遗传模式，并揭示了半克隆谱系之间存在高水平的杂合性。
西北部的物种分布范围有限，可能是在异域发生的物种形成，而东南部的物种分布范围更广，这与边缘物种形成或异域物种形成后二次接触一致。西北 Kimberley 地区的物种在形状上与东南部的物种不同，Kimberley 地区的物种明显比结实的东南部物种更长、更细，这可能是由于它们所栖息的河流的地形和水流模式不同。
