Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes.,Scientific Reports

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Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes.
Scientific Reports ( IF 3.8 ) Pub Date : 2020-02-18 , DOI: 10.1038/s41598-020-59544-9
Arni Sholihah _{1,

2} , Erwan Delrieu-Trottin _{2,

3} , Tedjo Sukmono ₄ , Hadi Dahruddin _{2,

5} , Renny Risdawati ₆ , Roza Elvyra ₇ , Arif Wibowo _{8,

9} , Kustiati Kustiati ₁₀ , Frédéric Busson _{2,

11} , Sopian Sauri ₅ , Ujang Nurhaman ₅ , Edmond Dounias ₁₂ , Muhamad Syamsul Arifin Zein ₅ , Yuli Fitriana ₅ , Ilham Vemendra Utama ₅ , Zainal Abidin Muchlisin ₁₃ , Jean-François Agnèse ₂ , Robert Hanner ₁₄ , Daisy Wowor ₅ , Dirk Steinke ₁₄ , Philippe Keith ₁₁ , Lukas Rüber _{15,

16} , Nicolas Hubert ₂

Affiliation

Instut Teknologi Bandung, School of Life Sciences and Technology, Bandung, Indonesia.
UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.
Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin, 10115, Germany.
Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122, Jambi, Sumatra, Indonesia.
Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia.
Department of Biology Education, STKIP PGRI Sumatera Barat, Jl Gunung Pangilun, Padang, 25137, Indonesia.
Universitas Riau, Department of Biology, Simpang Baru, Tampan, Pekanbaru, 28293, Indonesia.
Southeast Asian Fisheries Development Center, Inland Fisheries Resources Development and Management Department, 8 Ulu, Seberang Ulu I, Palembang, 30267, Indonesia.
Research Institute for Inland Fisheries and Fisheries extensions, Agency for Marine and Fisheries Research, Ministry of Marine Affairs and Fisheries., Jl. H.A. Bastari No. 08, Jakabaring, Palembang, 30267, Indonesia.
Universitas Tanjungpura, Department of Biology, Jalan Prof. Dr. H. Hadari Nawawi, Pontianak, 78124, Indonesia.
UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France.
UMR 5175 CEFE (IRD, UM, CNRS, EPHE), 1919 route de Mende, 34293, Montpellier, cedex, 05, France.
Syiah Kuala University, Faculty of Marine and Fisheries, Banda, Aceh, 23111, Indonesia.
Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada.
Naturhistorisches Museum Bern, Bernastrasse 15, Bern, 3005, Switzerland.
Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland.

Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.

中文翻译：

使用DNA条码解译Sun他兰（Rasborinae）子家族（Cypriniformes，Danionidae）的分类。

桑达兰岛是最大，最受威胁的生物多样性热点之一；但是，我们对其生物多样性的理解受到分类学和分配模式知识差距的困扰。Rasborinae亚科是Sun他兰最多样化的淡水鱼类。分类学和系统学的不确定性限制了它在进化研究中作为模型的使用。在这里，我们建立了Sundaland的Rasborinae的DNA条形码参考文库，以通过基于DNA的物种定界方法检查物种边界和范围分布。基于在线目录编制了Sun他兰树纲的清单，并用于估计本研究的分类学范围。我们从Sundaland的189个采样点生成了总共991条DNA条形码。我们与106个先前发布的序列一起，随后组装了一个1097个序列的参考文库，涵盖65个分类单元，其中包括79个已知的桑达兰（Rasborinae）物种中的61个。我们的图书馆表明，树莓属物种是由物种界定方法捕获的不同分子谱系定义的。观察到种内和种间遗传距离之间有很大的重叠，这可以由检测到的166个操作生物分类单位所证明的大量隐秘多样性来解释。讨论了物种多样化的进化动力学。我们的图书馆表明，树莓属物种是由物种界定方法捕获的不同分子谱系定义的。观察到种内和种间遗传距离之间有很大的重叠，这可以由检测到的166个操作生物分类单位所证明的大量隐秘多样性来解释。讨论了物种多样化的进化动力学。我们的图书馆表明，树莓属物种是由物种界定方法捕获的不同分子谱系定义的。观察到种内和种间遗传距离之间有很大的重叠，这可以由检测到的166个操作生物分类单位所证明的大量隐秘多样性来解释。讨论了物种多样化的进化动力学。

更新日期：2020-02-18

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