Mudskippers (Gobiidae: Oxudercinae): ecology and evolution along the water edge, and possible use as a biomonitor of tropical intertidal areas

Mudskippers (Gobiidae: Oxudercinae) are highly amphibious and closely related tropical gobies. Systematic, anatomical and physiological studies suggest that they increasingly adapted to semiterrestrial life throughout their evolution. Their physiological adaptations match ecological definitions based on environmental conditions of their habitats. Observations also suggest that synecological factors may be key selective agents. In this respect, recent palaeoecological and palaeontological findings suggest that mudskippers may help to understand some of the factors and processes that defined the scenario of the Devonian vertebrate eco-evolutionary transition. Mudskippers are also proposed as a biomonitor of the health and integrity of highly endangered mangrove and tropical tidal flat ecosystems, as suggested by their differential distribution along the intertidal zone. This also identifies them as possible flag species

Acoustic Communication at the Water's Edge: Evolutionary Insights from a Mudskipper

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

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

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 (<i>Scleropages formosus</i>) genome provides new insights into the evolution of an early lineage of teleosts

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

The Asian Arowana (Scleropages formosus) Genome Provides New Insights into the Evolution of an Early Lineage of Teleosts

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

Public perceptions of mangrove forests matter for their conservation

Abstract not available

Description of a new species of Periophthalmus (Teleostei: Gobiidae) from the Lesser Sunda Islands

Jaafar, Zeehan, Polgar, Gianluca, Zamroni, Yuliadi (2016): Description of a new species of Periophthalmus (Teleostei: Gobiidae) from the Lesser Sunda Islands. Raffles Bulletin of Zoology 64: 278-283, DOI: http://doi.org/10.5281/zenodo.535532

The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation

During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers&rsquo; demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy

Deceiving appearances: anthropogenic introgressive hybridization affects phenotypically-selected hatchery broodstock used in supportive breeding programmes of the critically endangered marble trout Salmo marmoratus, Cuvier (Osteichthyes, Salmoniformes, Salmonidae).

Anthropogenic introgressive hybridization is increasingly common in many ecosystems, with inland waters being particularly sensitive to bioinvasions of interfertile non-native taxa. Salmonid native populations are detrimentally affected by such human-induced secondary contacts in several countries promoting sport and commercial salmonid fisheries. In northern Italy, the Critically Endangered marble trout Salmo marmoratus Cuvier, 1829, is a species with exceptional cultural, economic, and conservation value. Supporting breeding programs based on phenotypic selection of wild-caught and captive broodstock is a widespread management practice to supplement local marble populations with both declared conservation and exploitation goals. Using mtDNA and nDNA markers (D-loop; 15 microsatellites) we compare a hatchery-bred sample of marble trout used as broodstock for support breeding with a smaller sample of wild-caught phenotypically selected individuals collected in the Toce River, a large glacial river within the Lake Maggiore basin (northern Italy and southern Switzerland). We measured genetic integrity and introgression levels with non-native Atlantic S. trutta, a non-native species massively introduced in the last two centuries. Consistent levels of introgression were found in these two samples, but asymmetrical introgression with higher mtDNA introgression levels was observed in hatchery-bred individuals. The detected genetic structure of wild-caught and domesticated stocks suggest that in synergy with potential domestication effects, inbreeding and genetic drift, caused by small number of founders and closed reproductive cycle, this practice can have negative effects on the genetic diversity and integrity of the wild population. On the other hand, our preliminary analysis of the Toce River sample suggests that this population may contain genetically pure individuals, thus acting as a key repository of genetic diversity for the long-term conservation of this species. The lack of correspondence between a set of coded coloration traits and genetic traits in both samples highlights the limits of using phenotypic selection during artificial breeding, as also supported by previous studies on this species. Our results strongly suggest to revise current supportive breeding programmes of the marble trout in this system. We finally propose possible future directions for the restoration and sustainable management of the genetic diversity of the Toce River marble trout population

Data from: Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)

This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The three datasets were then used to perform phylogeographic, demographic and population genetic analyses. Our results indicate that tectonic events and past climatic oscillations strongly contributed to shape present genetic differentiation, phylogeographic and demographic patterns. We found support for the monophyly of P. kalolo, and only shallow genetic differentiation between East-African and Indo-Malayan populations of this species. However, our collections of the morphospecies P. argentilineatus include three molecularly distinct lineages, one of them more closely related to P. kalolo. The presence of Miocenic timings for the most recent common ancestors of some of these morphologically similar clades, suggests the presence of strong stabilising selection in mudskippers’ habitats. At population level, demographic analyses and palaeoecological records of mangrove ecosystems suggest that Pleistocene bottlenecks and expansion plus secondary contact events of the studied species were associated with recurrent sea transgressions during interglacials, and sea regressions or stable regimes during glacials, respectively