1 SCIENTIFIC REPORTS | (2020) 10:192 | https://doi.org/10.1038/s41598-019-57042-1 www.nature.com/scientificreports A thirteen-million-year divergence between two lineages of Indonesian coelacanths Kadarusman 1,2 , Hagi Yulia Sugeha 3 , Laurent Pouyaud 4 , Régis Hocdé 5 , Intanurfemi B. Hismayasari 1 , Endang Gunaisah 1 , Santoso B. Widiarto 6 , Gulam Arafat 6 , Ferliana Widyasari 6 , David Mouillot 5 & Emmanuel Paradis 4* Coelacanth fshes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these ‘living fossils’ using new molecular data, including the possibility of ‘cryptic’ species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international efort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life. Coelacanth fshes of the genus Latimeria are the only living representatives of the Actinistia, a group of verte- brates that fourished between the Early Devonian (ca. 400 millions of years ago, Ma) and the Late Cretaceous (ca. 80 Ma) 1–3 . Fossil fshes belonging to the subclass Actinistia have been found around the world, whereas the two known living species of coelacanth are found only in the Western Indian Ocean (L. chalumnae 4 ) and in Indonesia (L. menadoensis 5 ). Sampling living specimens of coelacanths is a difcult endeavour, because they live at depths of 200 to 400 m although they occasionally occur at shallower depths of 100 m below the surface, while catches by fshermen are sporadic. Furthermore, direct observations suggest that coelacanths have a very sparse distribution and live in groups of a few tens of individuals 6–8 . Our current knowledge on the genetic diversity of these enigmatic animals suggests that L. chalumnae is distributed along several thousands kilometers of the South-East African coast and has very low genetic diversity based on mitochondrial genome markers 9,10 and on nuclear microsatellites 11 , whereas L. menadoensis is distributed in a very small area near the northern part of the island of Sulawesi, where only a few individuals have been studied genetically but show very close genetic afnities 12,13 (Fig. 1). Tese population genetic data strongly suggest that both species may represent the relicts of an ancient clade of early tetrapods decimated by extinctions 14 . Surprisingly, no specimens have been reported outside of these two restricted regions, while the existence of other coelacanth sub-species or species has never been mentioned. We here report results of the genetic analyses of a new coelacanth specimen, allegedly belonging to L. mena- doensis, caught recently in West Papua, Indonesia, approximately 750 km from Sulawesi. We fnd signifcant but Neogene-dated genetic diferences between this individual and populations of L. menadoensis found in Sulawesi, 1 Politeknik Kelautan dan Perikanan Sorong, KKD BP. SR SGK, Jl. Kapitan Pattimura, Tanjung Kasuari, Kota Sorong, 98401, Papua Barat, Indonesia. 2 Sekolah Tinggi Perikanan, KKD Pengelolaan Sumberdaya Perairan. SR BE, Jl. AUP, Pasar Minggu, Jakarta, 12520, Indonesia. 3 Research Center for Oceanography, Indonesian Institute of Sciences, Jl. Pasir Putih 1, Ancol Timur, Jakarta, 14430, Indonesia. 4 ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France. 5 MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France. 6 Loka Pengelolaan Sumberdaya Pesisir dan Laut Sorong, Jl. KPR PDAM, Km. 10, Kota Sorong, 98416, Papua Barat, Indonesia. *email: Emmanuel.Paradis@ird.fr OPEN Corrected: Publisher Correction