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The phylogenetic relationship between Amblyopinae and their closely related species in Gobioidei. The phylogeny was inferred from the amino acid sequences of 13 PCGs of the 63 Gobioidei mitogenomes examined using both Bayesian inference (BI) and maximum likelihood (ML) methods. Scalicus amiscus and Alosa sapidissima were used as the outgroups. The numbers on the branches are posterior probability (left) for Bayesian inference and bootstrap support (right) for ML analyses.
Source publication
The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clar...
Context in source publication
Context 1
... constructed the phylogeny of Amblyopinae using concatenated sequences of 13 coding sequences (CDSs) using our six newly sequenced mitogenomes and 57 published mitogenomes sequences from Gobioidei. The mitogenomic phylogenetic analyses yielded trees with consistent topologies and with high levels of support based on both ML and BI inference methods (Figure 3). Both the ML and BI trees indicated that species in the genera Amblyotrypauchen, Paratrypauchen, Ctenotrypauchen, Trypauchen, and Taenioides were more closely related to non-Amblyopinae species in the subfamily Oxudercinae than to species in the genus Odontamblyopus comprising their sister clade. ...
Citations
... These values are consistent with those recovered from other studies on closely related families, which are sister families of Mudskippers (Oxudercidae), including the subfamilies Amblyopinae Günther, 1861, Gobionellinae Bleeker, 1874, and Sicydiinae T.N. Gill, 1860 65,66 . The minimum and maximum ages, with 95% Highest Posterior Density (HPD) for individual and group node ages, are shown in Table 4. ...
Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.
... Here we re-sequenced 99 genomes and investigated patterns of genome-wide divergence between two closely related mudflat endemics, O. lacepedii and O. rebecca [13,14], spanning large contrasting latitude gradients of China to estimate the influence of selective processes of the climate in shaping genome-wide patterns of divergence. O. lacepedii and O. rebecca are two sub-economically important sister species belonging to the genus Odontamblyopus, Family Gobiidae of Gobiiformes [13]. ...
Deciphering the role of climate adaptation in generating genetic divergence and hence speciation is a central question in evolution. Comparisons of genomes of closely related species spanning selective climate gradients are particularly informative in discerning the signatures of selection and thereby providing valuable information concerning the role of climate adaptation in speciation. Here we re-sequenced 99 genomes of the two sister eel-goby species Odontamblyopus lacepedii and O. rebecca, which are endemic to tidal mudflats spanning contrasting latitude gradients, to estimate the influence of divergent climate selection on shaping genome-wide patterns of divergence. The results indicated that genome-wide differentiation between the two species was evident (genome-wide FST = 0.313). Against a background of high baseline genomic divergence, 588 and 1202 elevated divergent loci were detected to be widespread throughout their genomes, as opposed to focused within small islands of genomic regions. These patterns of divergence may arise from divergent climate selection in addition to genetic drift acting through past glacial segregation (1.46 million years ago). We identified several candidate genes that exhibited elevated divergence between the two species, including genes associated with substance metabolism, energy production, and response to environmental cues, all putative candidates closely linked to thermal adaptation expected from the latitude gradient. Interestingly, several candidates related to gamete recognition and time of puberty, and also exhibited elevated divergence, indicating their possible role in pre-zygote isolation and speciation of the two species. Our results would expand our knowledge on the roles of latitude climate adaptation and genetic drift in generating and maintaining biodiversity in marine teleosts.
... Positive selection can drive mitochondrial genes to better adapt to a symbiotic lifestyle. Previous studies have assigned positive selection signals detected in animal mitochondrial PCGs to oxygen usage and energy metabolism, as all 13 PCGs in a mitogenome are involved in aerobic metabolism (Sun et al., 2018;Shen et al., 2019;Lü et al., 2023). The branch-site model in this study identified multiple amino acid sites in different genes that experienced positive selection in gall crabs, pea crabs and the symbiotic varunids, although the support for positive selection in the latter two lineages was comparatively weak. ...
Background
Thoracotremata belong to the large group of “true” crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved.
Methods
Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi).
Results
The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.
... The water-to-land transition during the Paleozoic era was a major step in vertebrate evolution and eventually gave rise to the emergence of terrestrial animals [1,2]. After the bony fish firstly showed their terrestriality and active land-invasion, the ancestors of tetrapods successfully moved onto land [1,3]. ...
... One group of the bony fishes that show such seemly passive strategy of land conquest by living in mudflat burrow is Amblyopinae (Gobiiformes: Gobionellidae) [2,8], a portion of small elongate, mud-dwelling fishes of the Indo-West Pacific region that are commonly referred to as "eel gobies" [9]. They are usually found in deep burrows of tidal mudflats, muddy bottoms of estuaries, as well as substrates from the adjacent shallow waters [10]. ...
... The observation that Taenioides sp. was clustered with the active amphibious fish of P. magnuspinnatus rather than other teleost species, suggested that these two terrestrial lineage of the fish may have a common evolutionary origin. This assumption was further supported by results from multiple previous phylogenetic studies, showing their affinity among the two lineages [2,14]. Based on these evidences, Steppan [8] even suggested that these two terrestrial lineage of Amblyopinae and Oxudercinae should be merged into one subfamily under family Gobionellidae of Gobiiformes. in the phylogenetic tree was marked with a red star. ...
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.
Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumier i was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 pb of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri . The phylogenetic analysis grouped all mudskippers species as a monophyletic group and the analysis positioned the Periophthalmus clade as the most basal in the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.
