Beheregaray Luciano B, Pfeiffer Lauren V, Attard Catherine R M, Sandoval-Castillo Jonathan, Domingos Fabricius M C B, Faulks Leanne K, Gilligan Dean M, Unmack Peter J
Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia.
Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia.
Mol Phylogenet Evol. 2017 Jun;111:65-75. doi: 10.1016/j.ympev.2017.03.021. Epub 2017 Mar 24.
Species range limits often fluctuate in space and time in response to variation in environmental factors and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia. We generated ddRAD data (18,979 filtered SNPs and 1.725million bp of sequences) for samples from 27 localities spanning the native range of golden perch, Macquaria ambigua (Teleostei; Percichthyidae). Our analytical framework uses population genomics to assess connectivity and population structure using model-based and model-free approaches, phylogenetics to clarify evolutionary relationships, and a coalescent-based Bayesian species delimitation method to assess statistical support of inferred species boundaries. Addressing uncertainties regarding range limits and taxonomy is particularly relevant for this iconic Australian species because of the intensive stocking activities undertaken to support its recreational fishery and its predicted range shifts associated with ongoing climate change. Strong population genomic, phylogenetic, and coalescent species delimitation support was obtained for three separately evolving metapopulation lineages, each lineage should be considered a distinct cryptic species of golden perch. Their range limits match the climate-determined boundaries of main river basins, despite the ability of golden perch to cross drainage divides. We also identified cases suggestive of anthropogenic hybridization between lineages due to stocking of this recreationally important fish, as well as a potential hybrid zone with a temporally stable pattern of admixture. Our work informs on the consequences of aridification in the evolution of aquatic organisms, a topic poorly represented in the literature. It also shows that genome-scale data can substantially improve and rectify inferences about taxonomy, hybridization and conservation management previously proposed by detailed genetic studies.
物种分布范围的界限常常会随着环境因素的变化以及适应性特征改变所导致的生态位逐渐演变，在空间和时间上发生波动。我们利用全基因组数据，对一种广布且高度扩散的鱼类进行了进化分歧和物种分布范围界限的研究，该物种在澳大利亚干旱和半干旱地区呈现出异常广泛的分布。我们为来自27个地点的样本生成了ddRAD数据（18,979个过滤后的单核苷酸多态性位点和172.5万个碱基对的序列），这些地点涵盖了黄斑鲈（Macquaria ambigua，硬骨鱼纲；鲈科）的原生分布范围。我们的分析框架运用群体基因组学，通过基于模型和无模型的方法来评估连通性和种群结构，利用系统发育学来阐明进化关系，并采用基于溯祖理论的贝叶斯物种界定方法来评估推断出的物种边界的统计支持。由于为支持其休闲渔业而进行的密集放流活动以及与持续气候变化相关的预测分布范围变化，解决关于分布范围界限和分类学的不确定性对于这种标志性的澳大利亚物种尤为重要。我们获得了强有力的群体基因组、系统发育和溯祖物种界定支持，表明存在三个独立进化的集合种群谱系，每个谱系都应被视为黄斑鲈的一个独特隐存物种。尽管黄斑鲈有跨越水系分水岭的能力，但其分布范围界限与气候决定的主要流域边界相匹配。我们还发现了一些迹象，表明由于对这种具有重要休闲价值的鱼类进行放流，不同谱系之间存在人为杂交现象，以及一个具有时间上稳定混合模式的潜在杂交带。我们的研究揭示了干旱化对水生生物进化的影响，这是文献中较少涉及的一个主题。它还表明，基因组规模的数据可以显著改进和纠正先前详细遗传研究中提出的关于分类学、杂交和保护管理的推断。
