Genomic architecture of Shh-dependent cochlear morphogenesis.

The mammalian cochlea develops from a ventral outgrowth of the otic vesicle in response to Shh signaling. Mouse embryos lacking Shh or its essential signal transduction components display cochlear agenesis; however, a detailed understanding of the transcriptional network mediating this process is unclear. Here, we describe an integrated genomic approach to identify Shh-dependent genes and associated regulatory sequences that promote cochlear duct morphogenesis. A comparative transcriptome analysis of otic vesicles from mouse mutants exhibiting loss (Smoecko ) and gain (Shh-P1) of Shh signaling reveal a set of Shh-responsive genes partitioned into four expression categories in the ventral half of the otic vesicle. This target gene classification scheme provides novel insight into several unanticipated roles for Shh, including priming the cochlear epithelium for subsequent sensory development. We also mapped regions of open chromatin in the inner ear by ATAC-seq that, in combination with Gli2 ChIP-seq, identified inner ear enhancers in the vicinity of Shh-responsive genes. These datasets are useful entry points for deciphering Shh-dependent regulatory mechanisms involved in cochlear duct morphogenesis and establishment of its constituent cell types.

Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus.

In the developing brain, growth and differentiation are intimately linked. Here, we show that in the zebrafish embryo, the homeodomain transcription factor Rx3 coordinates these processes to build the tuberal/anterior hypothalamus. Analysis of rx3 chk mutant/rx3 morphant fish and EdU pulse-chase studies reveal that rx3 is required to select tuberal/anterior hypothalamic progenitors and to orchestrate their anisotropic growth. In the absence of Rx3 function, progenitors accumulate in the third ventricular wall, die or are inappropriately specified, the shh(+) anterior recess does not form, and its resident pomc(+), ff1b(+) and otpb(+) Th1(+) cells fail to differentiate. Manipulation of Shh signalling shows that Shh coordinates progenitor cell selection and behaviour by acting as an on-off switch for rx3 Together, our studies show that Shh and Rx3 govern formation of a distinct progenitor domain that elaborates patterning through its anisotropic growth and differentiation.

Evolution of life history traits in Asian freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) based on multilocus molecular phylogenetic analysis.

Freshwater prawns of the genus Macrobrachium are free-living decapod crustaceans that are commonly encountered in tropical streams and lakes. We present a molecular phylogenetic analysis of the diverse Southeast and East Asian fauna based on >3 kb sequence data from three nuclear and two mitochondrial markers for almost 50% of the described fauna. We reconstruct the phylogenetic relationships and track the evolution of key life history traits. Our tree suggests that the last common ancestor of the Asian Macrobrachium laid numerous small eggs and had prolonged larval development ("PLD") in saline coastal waters after which the adults matured in freshwater habitats. We also argue for five independent losses of the marine larval phase to yield five clades of species that develop entirely in freshwater and have fewer and larger eggs than the species with PLD. These species have either semi-abbreviated (two origins) with at least one free-swimming stage or abbreviated larval development ("ALD": three origins) which lack free-swimming larvae. A Shimodaira-Hasegawa test rejects all trees that would imply a single loss of the marine larval phase, but alternative and equally parsimonious optimizations exist that imply a smaller number of losses. However, these scenarios would require the re-acquisition of free-swimming larvae. A concentrated-change test supports Pereira and Garcia's [Pereira, G.A., Garcia, J.V., 1995. Larval development of Macrobrachium reyesi Pereira (Decapoda, Palaemonidae), with a discussion on the origin of abbreviated development in palaemonids. J. Crust. Biol. 15, 117-133] hypothesis of a significant correlation between living in freshwater and the origin of semi-abbreviated and abbreviated larval development. Our phylogenetic tree also reveals that Asian Macrobrachium have independently become cavernicolous at least twice, and invaded the highly acidic waters of freshwater and peat swamps two or three times.