Hybridization and introgression between closely related species significantly affect their evolutionary and ecological processes. Understanding the ecological, environmental, and geographical conditions that promote their occurrence is imperative. It is hypothesized that species inhabiting geologically unstable habitats or with life-history constraints that prevent evasion from such environments are more prone to interspecific hybridization, due to limited development of prezygotic isolation. To test this hypothesis, we conducted a comparative analysis of genome-wide hybridization patterns in two freshwater goby groups of Gymnogobius: the castaneus- and urotaenia-groups. Utilizing the newly determined draft genome of G. isaza and single nucleotide variants identified by RNA sequencing, we first established the species phylogeny and then examined genetic signatures of interspecific hybridization in each group. The results revealed that all castaneus-group species, which primarily inhabit unstable habitats such as ponds, have undergone interspecific hybridization. Conversely, no species of the urotaenia-group showed clear evidence of hybridization over a period of more than 1 million years. These species inhabit an ancient lake (one species) or rivers (three amphidromous species), the latter possessing potential dispersal abilities in early life to evade geological disturbances. These ecology-geology relationships have remarkable implications for the intricate processes of adaptation and speciation.

Warning coloration and Batesian mimicry are classic examples of Darwinian evolution, but empirical evolutionary patterns are often paradoxical. We test whether foraging costs predict the evolution of striking coloration by integrating genetic and ecological data for aposematic and mimetic snakes (Elapidae and Dipsadidae). Our phylogenetic comparison on a total of 432 species demonstrated that dramatic changes in coloration were well predicted by foraging strategy. Multiple tests consistently indicated that warning coloration and conspicuous mimicry were more likely to evolve in species where foraging costs of conspicuous appearance were relaxed by poor vision of their prey, concealed habitat, or nocturnal activity. Reversion to crypsis was also well predicted by ecology for elapids but not for dipsadids. In contrast to a theoretical prediction and general trends, snakes' conspicuous coloration was correlated with secretive ecology, suggesting that a selection regime underlies evolutionary patterns. We also found evidence that mimicry of inconspicuous models (pitvipers) may have evolved in association with foraging demand for crypsis. These findings demonstrate that foraging is an important factor necessary to understand the evolution, persistence, and diversity of warning coloration and mimicry of snakes, highlighting the significance of additional selective factors in solving the warning coloration paradox.

BackgroundFloodplains harbor highly biodiverse ecosystems, which have been strongly affected by both past climate change and by recent human activities, resulting in a high prevalence of many endangered species in these habitats. Understanding the history of floodplain species over a wide range of timescales can contribute to effective conservation planning. We reconstructed the population formation history of the Itasenpara bitterling Acheilognathus longipinnis, an endangered floodplain fish species in Japan, over a broad timescale based on phylogenetic analysis, demographic modeling, and historical demographic analysis using mitogenome and whole-genome sequences. A genome sequence was newly assembled as a reference for the resequencing analysis. This bitterling is distributed in three plains separated by high mountain ranges and exhibits ecological characteristics well adapted to floodplain environments.ResultsOur analyses revealed an unexpected population branching pattern, gene flow, and timing of the differentiation that occurred within a few hundred thousand years, i.e., long after the mountain uplift that was assumed to be the primary geological cause of the population differentiation. The analyses also showed that all local populations experienced a severe decline during the last glacial and post-glacial periods.ConclusionsOur results suggest that the floodplain bitterling was able to disperse through unknown routes after mountain uplift and that its populations were strongly influenced by climatic and geographic changes in glacial-interglacial cycles and subsequent human activities, probably related to its floodplain-dependent ecology. The genomic data highlight the unanticipated distribution process of this species and the magnitude of the impact of human activities, with important implications for its conservation.

Colonisation of freshwater habitats by marine animals is a remarkable evolutionary event that has enriched biodiversity in freshwater ecosystems. The acquisition of tolerance to hypotonic stress during early life stages is presumed to be essential for their successful freshwater colonisation, but very little empirical evidence has been obtained to support this idea. This study aimed to comprehend the evolutionary changes in osmoregulatory mechanisms that enhance larval freshwater tolerance in amphidromous fishes, which typically spend their larval period in marine (ancestral) habitats and the rest of their life history stages in freshwater (derived) habitats. We compared the life history patterns and changes in larval survivorship and gene expression depending on salinity among three congeneric marine-originated amphidromous goby species (Gymnogobius), which had been suggested to differ in their larval dependence on freshwater habitats. An otolith microchemical analysis and laboratory-rearing experiment confirmed the presence of freshwater residents only in G. urotaenia and higher larval survivorship of this species in the freshwater condition than in the obligate amphidromous G. petschiliensis and G. opperiens. Larval whole-body transcriptome analysis revealed that G. urotaenia from both amphidromous and freshwater-resident populations exhibited the greatest differences in expression levels of several osmoregulatory genes, including aqp3, which is critical for water discharge from their body during early fish development. The present results consistently support the importance of enhanced freshwater tolerance and osmoregulatory plasticity in larval fish to establish freshwater forms, and further identified key candidate genes for larval freshwater adaptation and colonisation in the goby group.

Colonisation of freshwater habitats by marine animals is a remarkable evolutionary event that has enriched biodiversity in freshwater ecosystems. For successful freshwater colonisation, high physiological plasticity is presumed to be necessary, but its evolutionary basis has not been detailed. Marine-originated amphidromous species, which regularly migrate between freshwater and marine environments, have repeatedly lost migratory behaviour in many lineages, which sometimes triggered species radiation in freshwater habitats. Since amphidromous species typically visit the sea during the larval period, the difficulty in the evolution of larval freshwater tolerance is a bottleneck for freshwater colonisation. To elucidate the key evolutionary changes that enhance the physiological plasticity for freshwater colonisation, we compared larval gene expression changes depending on salinity conditions among three congeneric amphidromous goby species (Gymnogobius) with varying dependences on freshwater habitats. First, an otolith microchemical analysis and rearing experiment under laboratory conditions confirmed the presence of freshwater residents only in G. urotaenia and higher larval survivorship of this species both in seawater and freshwater conditions than the obligate amphidromous G. petschiliensis and G. opperiens. Larval whole-body transcriptome analysis revealed that G. urotaenia exhibited the greatest differences in the expression levels of several osmoregulatory genes, including aqp3, which is critical for water discharge from their body during early fish development. Thus, we obtained the results that consistently support the importance of enhanced osmoregulatory plasticity for establishing freshwater forms, and further identified some important evolutionary changes for larval freshwater adaptation and colonisation in the goby group.

Adaptive evolution of vision-related genes has been frequently observed in the process of invasion of new environments in a wide range of animal taxa. The typical example is that of the molecular evolution of rhodopsin associated with habitat changes in aquatic animals. However, few studies have investigated rhodopsin evolution during adaptive radiation across various habitats. In the present study, we examined the link between molecular evolutionary patterns in the rhodopsin gene and macroscopic habitat changes in Gymnogobius species (Gobiidae), which have adaptively radiated to diverse aquatic habitats including the sea, brackish waters, rivers and lakes. Analysis of amino acid substitutions in rhodopsin in the phylogenetic framework revealed convergent substitutions in 4-5 amino acids in three groups (four species), including two spectral tuning amino acid sites known to change rhodopsin's absorption wavelength. Positive selection was detected in the basal branches of each of these three groups, suggesting adaptive molecular convergence of rhodopsin. However, no significant correlation was observed between amino acid substitutions and the species' habitat changes, suggesting molecular adaptation to some unidentified micro-ecological environments. Taken together, these results emphasize the importance of considering not only macroscopic habitats but also micro-ecological environments when elucidating the driving forces of adaptive evolution of the visual system.