Exploring community assembly among Javanese and Balinese freshwater shrimps (Atyidae, Palaemonidae) through DNA barcodes

  • Rena Hernawati
  • Ujang Nurhaman
  • Frédéric Busson
  • Bambang Suryobroto
  • Robert Hanner
  • Philippe Keith
  • Daisy Wowor
  • Nicolas HubertEmail author
Primary Research Paper


Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the relative contribution of evolutionary and ecological dynamics might be a difficult task, particularly so for the tropical biotas due to their extreme diversity and large knowledge gaps. Here, we explore genetic diversity and distribution of 23 freshwater shrimp species of the genera Caridina and Macrobrachium in Sundaland to examine patterns of species co-occurrence based on 1583 observations across 19 sites in Java and Bali islands. DNA-based species delimitation methods applied to 204 cytochrome oxidase I sequences detected 30 operational taxonomic units and a few cases of deep intraspecific divergence. Species co-occurrence and phylogenetic community structure show no departure from expectations under a random distribution of species in landscapes and support a lottery model of community assembly. Species age estimates expand beyond the geological settlement of Sundaland, suggesting that species proliferation and community assembly are driven by mechanisms acting at distinct spatial and temporal scales.


Caridina Macrobrachium Species delimitation Dispersal Phylogenetic community structure Lottery model 



The authors wish to thank Dr. Siti Nuramaliati Prijono, Dr. Bambang Sunarko, Dr. Witjaksono, Mohammad Irham Msc., Dr. Marlina Adriyani, Ruliyana Susanti, Dr. Rosichon Ubaidillah, Dr. Hari Sutrisno and Muhamad Syamsul Arifin Zein Msc, at Research Centre for Biology (RCB-LIPI); Jean-Paul Toutain, Robert Arfi, Valérie Verdier and Jean-François Agnèse from the “Institut de Recherche pour le Développement”; Joel Le Bail and Nicolas Gascoin at the French embassy in Jakarta for their continuous support. We are thankful to late Renny Kurnia Hadiaty and Sopian Sauri at RCB-LIPI, Sumanta at IRD Jakarta for their help during the field sampling in East Java and Bali. Part of the present study was funded by the Institut de Recherche pour le Développement (UMR 226 ISEM and IRD through incentive funds), the MNHN (UMR BOREA), the RCB-LIPI, the French Ichthyological Society (SFI), the Foundation de France and the French embassy in Jakarta. The Indonesian Ministry of Research and Technology approved this study, and field sampling was conducted according to the research permits 097/SIP/FRP/SM/IV/2014 for Philippe Keith, 60/EXT/SIP/FRP/SM/XI/2014 for Frédéric Busson and 41/EXT/SIP/FRP/SM/VIII/2014 for Nicolas Hubert. Sequence analysis was aided by funding from the government of Canada through Genome Canada and the Ontario Genomics Institute in support of the International Barcode of Life project. We thank Paul Hébert and Evgeny Zakharov as well as BOLD and CCDB staffs at the University of Guelph for their valuable support. We are also very grateful to our editor, Diego Fontaneto, as well as the two anonymous reviewers for their insightful feedbacks on the earlier version of the manuscript. This publication has ISEM Number 2019-189 SUD.

Supplementary material

10750_2019_4127_MOESM1_ESM.pdf (48 kb)
Neighbor-joining phenogram based on the 204 individual COI sequences. Supplementary material 1 (PDF 48 kb)
10750_2019_4127_MOESM2_ESM.xlsx (12 kb)
Occurrence data for the 23 species included in the present study and based on 1583 observations across 19 sites. Supplementary material 2 (XLSX 11 kb)
10750_2019_4127_MOESM3_ESM.xlsx (58 kb)
Details of BOLD records for the 204 specimens with a COI sequence. Supplementary material 3 (XLSX 58 kb)
10750_2019_4127_MOESM4_ESM.xlsx (17 kb)
Details of the species delimitation schemes. Supplementary material 4 (XLSX 16 kb)
10750_2019_4127_MOESM5_ESM.xlsx (12 kb)
Occurrence data for the 30 OTUs detected in the present study across the 19 sites. Supplementary material 5 (XLSX 12 kb)


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Authors and Affiliations

  1. 1.Division of ZoologyResearch Center for Biology, Indonesian Institute of Sciences (LIPI)CibinongIndonesia
  2. 2.Faculty of Mathematics and Natural Science, Animal BioscienceBogor Agricultural UniversityBogorIndonesia
  3. 3.UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d’Histoire NaturelleParis Cedex 05France
  4. 4.Department of Integrative BiologyUniversity of GuelphGuelphCanada
  5. 5.UMR 5554 ISEM (IRD-UM-CNRS-EPHE), Institut de Recherche pour le Développement, Université de Montpellier, CNRS, IRD, EPHEMontpellier Cedex 05France

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