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Background  Within Malacostraca (Crustacea), direct development and development through diverse forms of larvae are found. Recent investigations suggest that larva-related developmental features have undergone heterochronic evolution in Malacostraca. In the light of current phylogenetic hypotheses, the free-swimming  nauplius  larva was lost in the lineage leading to Malacostraca and evolved convergently in the malacostracan groups Dendrobranchiata and Euphausiacea. Here we reconstruct the evolutionary history of eumalacostracan (Malacostraca without Phyllocarida) development with regard to early appendage morphogenesis, muscle and central nervous system development, and determine the heterochronic transformations involved in changes of ontogenetic mode.    Results  Timing of 33 developmental events from the different tissues was analyzed for six eumalacostracan species (material for Euphausiacea was not available) and one outgroup, using a modified version of  Parsimov - based genetic inference  (PGi). Our results confirm previous suggestions that the event sequence of  nauplius  larva development is partly retained in embryogenesis of those species which do not develop such a larva. The ontogenetic mode involving a  nauplius  larva was likely replaced by direct development in the malacostracan stem lineage. Secondary evolution of the  nauplius  larva of Dendrobranchiata from this ancestral condition, involved only a very small number of heterochronies, despite the drastic change of life history. In the lineage leading to Peracarida, timing patterns of  nauplius -related development were lost. Throughout eumalacostracan evolution, events related to epidermal and neural tissue development were clearly less affected by heterochrony than events related to muscle development.    Conclusions  Weak integration between mesodermal and ectodermal development may have allowed timing in muscle formation to be altered independently of ectodermal development. We conclude that heterochrony in muscle development played a crucial role in evolutionary loss and secondary evolution of a  nauplius  larva in Malacostraca.    Electronic supplementary material  The online version of this article (doi:10.1186/2041-9139-6-4) contains supplementary material, which is available to authorized users.

Evolution of eumalacostracan development—new insights into loss and reacquisition of larval stages revealed by heterochrony analysis