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Genetica

, Volume 143, Issue 2, pp 195–205 | Cite as

An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods

  • L. Aznar-Cormano
  • J. Brisset
  • T.-Y. Chan
  • L. Corbari
  • N. Puillandre
  • J. Utge
  • M. Zbinden
  • D. Zuccon
  • S. Samadi
Article

Abstract

During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection among those available for Decapoda. Here we test in the Caridea if improving the taxonomic coverage following the hierarchical scheme of the classification, as it is currently accepted, provides a better phylogenetic resolution for the inter-families relationships. The rich collections of the Muséum National d’Histoire Naturelle de Paris are used for sampling as far as possible at least two species of two different genera for each family or subfamily. All potential markers are tested over this sampling. For some coding genes the amplification success varies greatly among taxa and the phylogenetic signal is highly saturated. This result probably explains the taxon-heterogeneity among previously published studies. The analysis is thus restricted to the genes homogeneously amplified over the whole sampling. Thanks to the taxonomic sampling scheme the monophyly of most families is confirmed. However the genes commonly used in Decapoda appear non-adapted for clarifying inter-families relationships, which remain poorly resolved. Genome-wide analyses, like transcriptome-based exon capture facilitated by the new generation sequencing methods might provide a sounder approach to resolve deep and rapid radiations like the Caridea.

Keywords

Caridea Phylogeny Museum specimens 

Notes

Acknowledgments

We are grateful to Bertrand Richer de Forges and Philippe Bouchet, cruise leaders of several deep-sea cruises of the Tropical Deep-Sea Benthos program on board R/V Alis, that generated most of the samples used in this study. We also thank Philippe Keith for providing freshwater species and Pierre Chevaldonné for the specimens of Bresilia saldanhai. All material has been collected under appropriate collection permits and approved ethics guidelines. This Project was supported by the network “Bibliothèque du Vivant” funded by the CNRS, the Muséum National d’Histoire Naturelle, the INRA and the CEA (Genoscope), the French-Taiwanese Project TF-DeepEvo funded by ANR (ANR 12-ISV7-0005-01) and Ministry of Science and Technology, Taiwan, R.O.C., and the project “Taxonomie moléculaire: DNA Barcode et gestion durable des collections” funded by the Muséum National d’Histoire Naturelle.

Conflict of interest

None.

Supplementary material

10709_2014_9807_MOESM1_ESM.doc (62 kb)
Supplementary material 1 (DOC 62 kb)
10709_2014_9807_MOESM2_ESM.xls (114 kb)
Supplementary material 2 (XLS 115 kb)

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • L. Aznar-Cormano
    • 1
  • J. Brisset
    • 2
  • T.-Y. Chan
    • 3
  • L. Corbari
    • 1
  • N. Puillandre
    • 1
  • J. Utge
    • 4
  • M. Zbinden
    • 5
  • D. Zuccon
    • 1
    • 4
  • S. Samadi
    • 1
  1. 1.ISYEB - UMR 7205 – CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Département Systématique et EvolutionSorbonne UniversitésParis Cedex 05France
  2. 2.Direction des CollectionsMuséum National d’Histoire NaturelleParisFrance
  3. 3.Institute of Marine Biology and Centre of Excellence for the OceansNational Taiwan Ocean UniversityKeelungTaiwan
  4. 4.Service de Systématique Moléculaire, UMS2700 MNHN-CNRS, Département Systématique et EvolutionMuséum National d’Histoire NaturelleParisFrance
  5. 5.Biologie des Organismes Aquatiques et Ecosystèmes, UMR7208, MNHN-CNRS-IRD-UPMCMuséum National d’Histoire NaturelleParisFrance

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