Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers’ tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.

The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas.

Mudskippers (Gobiidae: Oxudercinae) are amphibious gobies. The occurrence and habitats of seven sympatric species of Malayan mudskippers were recorded: Boleophthalmus boddarti, Boleophthalmus pectinirostris, Periophthalmodon schlosseri, Periophthalmus chrysospilos, Periophthalmus gracilis, Periophthalmus variabilis and Scartelaos histophorus. A total of 14 surveys were made at six localities along 120 km of the west coast of the Malay Peninsula in August 1996 and September 2006. A multivariate set of ordinal parameters were used to measure the quantity of environmental water in mudskippers' habitats, and three guilds of species were discriminated. The resulting pattern mirrored the adaptive scenario depicted by physiological and anatomical studies of mudskippers' terrestriality, although in one case a terminal taxon was less terrestrial than other more basal ones. Differentiation of trophic niches may also play a role in habitat selection by the herbivorous Boleophthalmus spp., which were only found in unvegetated, illuminated areas and on wet mud at low tide. With the more terrestrial guild, a significant negative co-occurrence suggested direct interspecific competition

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Coupled behavioural observations and acoustical recordings of aggressive dyadic contests showed that the mudskipper Periophthalmodon septemradiatus communicates acoustically while out of water. An analysis of intraspecific variability showed that specific acoustic components may act as tags for individual recognition, further supporting the sounds' communicative value. A correlative analysis amongst acoustical properties and video-acoustical recordings in slow-motion supported first hypotheses on the emission mechanism. Acoustic transmission through the wet exposed substrate was also discussed. These observations were used to support an “exaptation hypothesis”, i.e. the maintenance of key adaptations during the first stages of water-to-land vertebrate eco-evolutionary transitions (based on eco-evolutionary and palaeontological considerations), through a comparative bioacoustic analysis of aquatic and semiterrestrial gobiid taxa. In fact, a remarkable similarity was found between mudskipper vocalisations and those emitted by gobioids and other soniferous benthonic fishes.

During several surveys made in the region of the lower Fly River and delta, Papua New Guinea, nine species of oxudercine gobies (Gobiidae: Oxudercinae) were recorded: Boleophthalmus caeruleomaculatus, Oxuderces wirzi, Periophthalmodon freycineti, Periophthalmus darwini, Periophthalmus novaeguineaensis, Periophthalmus takita, Periophthalmus weberi, Scartelaos histophorus and Zappa confluentus. An exploratory multivariate analysis of their habitat conditions discriminated five guilds, differentially distributed in habitats with different quantities of environmental water and three guilds corresponding to different levels of salinity. A partial correspondence between phylogenetic and ecological categories suggested the presence of parallel adaptive radiations within different genera. In particular, the species found in the most terrestrial habitats (P. weberi) was also found in the widest range of conditions, suggesting that colonization of extreme semi-terrestrial and freshwater habitats by this species was facilitated by eurytypy. It is proposed that these findings provide insight into convergent adaptations for the vertebrate eco-evolutionary transition from sea to land.

Reduction in size from sea to land is a common trend of many fish species and communities, at both the intraspecific and interspecific level. Within the intertidal zone, similar trends have been described at the intraspecific level in several transient and resident fish species. Oxudercines are a group of intertidal gobies (Gobiidae: Oxudercinae) including several species, which exhibit extreme adaptations to an amphibious lifestyle. Ecomorphological and ecophysiological considerations suggest that size reduction in this group may have facilitated the adaptation to semi-terrestrial conditions. To test this hypothesis, the spatial ecology and the presence of an intra-and interspecific size gradient was investigated in an oxudercine community of a Malayan intertidal ecosystem (6 species included in 3 genera). A random stratified sampling design was adopted, and ANOVA and cluster analysis performed to describe this variation. Multivariate analyses of the quantity of environmental water were also conducted to investigate the correspondence between size and habitat terrestriality. Larger species were found in more aquatic conditions at lower topographical levels along the vertical intertidal gradient, supporting the hypothesis of an adaptive value of smaller size in more terrestrial habitats. Intraspecific variation showed more complex patterns, even if in several species smaller individuals were found in more terrestrial conditions.

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