Monsoon boosted radiation of the endemic East Asian carps

Major historical events often trigger the rapid flourishing of a few lineages,which in turn shape established biodiversity patterns.How did this process occur and develop?This study provides a window into this issue.The endemic East Asian carps(EEAC)dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems.A series of evidence,including ecogeography,phylogenetics,and macroevolution,suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities.We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting(e.g.,marine transgression and regression and glacial-interglacial cycle)have further reshaped the distribution patterns of EEAC’s members.Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting,which boosted radiation.Overall,this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.

Enlarged fins of Tibetan catfish provide new evidence of adaptation to high plateau

The uplift of the Tibetan Plateau significantly altered the geomorphology and climate of the Euroasia by creating large mountains and rivers.Fishes are more likely to be affected relative to other organisms,as they are largely restricted to river systems.Faced with the rapidly flowing water in the Tibetan Plateau,a group of catfish has evolved greatly enlarged pectoral fins with more numbers of fin-rays to form an adhesive apparatus.However,the genetic basis of these adaptations in Tibetan catfishes remains elusive.In this study,we performed comparative genomic analyses based on the chromosome-level genome of Glyptosternum maculatum in family Sisoridae and detected some proteins with conspicuously high evolutionary rates in particular in genes involved in skeleton development,energy metabolism,and hypoxia response.We found that the hoxd12a gene evolved faster and a loss-of-function assay of hoxd12a supports a potential role for this gene in shaping the enlarged fins of these Tibetan catfishes.Other genes with amino acid replacements and signatures of positive selection included proteins involved in low temperature(TRMU)and hypoxia(VHL)responses.Functional assays reveal that the G.maculatum TRMU allele generates more mitochondrial ATP than the ancestral allele found in low-altitude fishes.Functional assays of VHL alleles suggest that the G.maculatum allele has lower transactivation activity than the low-altitude forms.These findings provide a window into the genomic underpinnings of physiological adaptations that permit G.maculatum to survive in the harsh environment of the Tibetan Himalayas that mirror those that are convergently found in other vertebrates such as humans.

3D landscape reorganization in response to feeding preferences adaptation in the youngest split Gymnocypris fish

Divergence in feeding preference is one of the main mechanisms that lead to the emergence of new species.However,little is known about the underlying genetic mechanism of feeding preference adaptation,especially in the three-dimensional(3D)chromatin organization regulation.Gymnocypris eckloni scoliostomus(GS)and G.eckloni eckloni(GE)are two sister species of G.eckloni(Cyprinidae:Schizothoracinae:Gymnocypris).

Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae

Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.