Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Yu; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tang, Y. Tom; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lü, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhong‐Jian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L.; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

doi:10.1038/ncomms6594

Cited by 154 publications

(220 citation statements)

References 54 publications

(56 reference statements)

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“…The most similar part of the result of our study with above‐mentioned studies is that in all of them, Periophthalmus is classified in a separate clade, and the other genera of subfamilies Oxudercinae and Amblyopinae are nested in another clade. Scartelaos and Boleophthalmus genera are sister taxa based on whole genome sequencing (You et al., ), and our phylogenetic tree is congruent with this result that the two species of Scartelaos and three species of Boleophthalmus are classified as sister taxa based on new COI and cytb sequences (Fig. ).…”

Section: Discussionsupporting

confidence: 89%

Molecular phylogeny of three mudskippers (Gobiidae) from the Persian Gulf and Gulf of Oman (Makran)

et al. 2016

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Presented is a phylogenetic reconstruction of mudskippers using sequences of the mitochondrial COI and cytb genes. The phylogeny combines the sequences of 12 species from GenBank with those of three species (Boleophthalmus dussumieri, Periophthalmus waltoni and Scartelaos tenuis) collected from the coastal area of the Persian Gulf and Oman (Makran) Sea and sequenced for the first time. Based on the Maximum likelihood and Bayesian methods, Periophthalmus forms a separate clade that is the sister lineage to a group formed by all remaining genera. The subfamilies Oxudercinae and Amblyopinae established on the basis of morphological characters have been shown to be paraphyletic and their use as taxonomic units is no longer recommended. The evolution of Periophthalmus waltoni, Periophthalmus barbarous and Boleophthalmus dussumieri is discussed based on molecular phylogenetic reconstruction.

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Section: Discussionsupporting

confidence: 89%

Molecular phylogeny of three mudskippers (Gobiidae) from the Persian Gulf and Gulf of Oman (Makran)

et al. 2016

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“…Studies looking at the impact of selection on vertebrate immune genes have focused so far on expression changes after pathogen infection (Savage et al 2014), comparison of immune repertoires between vertebrate taxa (You et al 2014) or inferences of selection based on sequence divergence between taxa (Ekblom et al 2010). Despite the importance of the clawed frogs of genus Xenopus as a model for evolutionary and comparative immunobiology (Robert and Cohen 2011), patterns of variation and selective landscapes in amphibian immune genes are poorly known.…”

Section: Introductionmentioning

confidence: 99%

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

Fijarczyk¹,

Dudek²,

Babik³

2016

Genome Biol Evol

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Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.

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“…Active NH 4 + excretion into acidified branchial water in emersed P. schlosseri is thought to be the main mechanism of nitrogen excretion (Chew et al, 2007). Although the exact transport mechanisms have not been identified in mudskippers, active NH 4 + transport probably involves ammonia transporters (You et al, 2014) and mitochondria-rich cells (Randall et al, 2004).…”

Section: Nitrogen Excretionmentioning

confidence: 99%

Amphibious fishes: evolution and phenotypic plasticity

Wright

Turko

2016

Journal of Experimental Biology

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Amphibious fishes spend part of their life in terrestrial habitats. The ability to tolerate life on land has evolved independently many times, with more than 200 extant species of amphibious fishes spanning 17 orders now reported. Many adaptations for life out of water have been described in the literature, and adaptive phenotypic plasticity may play an equally important role in promoting favourable matches between the terrestrial habitat and behavioural, physiological, biochemical and morphological characteristics. Amphibious fishes living at the interface of two very different environments must respond to issues relating to buoyancy/gravity, hydration/ desiccation, low/high O 2 availability, low/high CO 2 accumulation and high/low NH 3 solubility each time they traverse the air-water interface. Here, we review the literature for examples of plastic traits associated with the response to each of these challenges. Because there is evidence that phenotypic plasticity can facilitate the evolution of fixed traits in general, we summarize the types of investigations needed to more fully determine whether plasticity in extant amphibious fishes can provide indications of the strategies used during the evolution of terrestriality in tetrapods.

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Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes

Cited by 154 publications

References 54 publications

Molecular phylogeny of three mudskippers (Gobiidae) from the Persian Gulf and Gulf of Oman (Makran)

Molecular phylogeny of three mudskippers (Gobiidae) from the Persian Gulf and Gulf of Oman (Makran)

Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation

Amphibious fishes: evolution and phenotypic plasticity

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