In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-β-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns.

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) is one of the most destructive rice pests and has caused serious economic losses in China. To clarify the genetic differentiation and population genetic structure of this insect pest, we investigated the genomic polymorphisms, genetic differentiation, and phylogeography of 31 SBPH populations from 28 sampling sites from three climatic zones of China using double-digest restriction site-associated DNA sequencing (ddRADseq). In total, 2,813,221,369 high-quality paired-end reads from 306 individuals and 1925 single nucleotide polymorphisms (SNPs) were obtained. Low levels of genetic diversity and significant genetic differentiation were observed among the SBPH populations, and three genetic clusters were detected in China. Neutrality tests and bottleneck analysis provided strong evidence for recent rapid expansion with a severe bottleneck in most populations. Our work provides new insights into the genetics of the SBPH and will contribute to the development of effective management strategies for this pest.

We present a high‐quality genome assembly for the Asiatic toad (Bufo gargarizans) and explore the evolution of several large gene families in amphibians. With a large genome assembly size of 4.55 Gb, the chromosome‐scale assembly includes 747 scaffolds with an N50 of 539.8 Mb and 1.79% gaps. Long terminal repeats (LTRs) constitute a high proportion of the genome and their expansion is a key contributor to the inflated genome size in this species. This is very different from other small amphibian genomes, but similar to that of the enormous axolotl genome. The genome retains a large number of duplicated genes, with tandem (TD) and proximal duplications (PD) the predominant mode of duplication. A total of 122 gene families have undergone significant expansion and were mainly enriched in sensory perception of smell and bitter taste. The CYP2C subfamily, which plays an important role in metabolic detoxification, specifically expanded via TD and PD in the Asiatic toad and the cane toad (true toads). Most of Na+/K+‐ATPase genes experienced accelerated evolution along Bufonid lineages and two amino acid sites involving toad‐toxin resistance were found to experience positive selection. We also revealed a dynamic evolution of olfactory and vomeronasal receptor gene families which was likely driven by the water‐to‐land transition. The high‐quality genome of the Asiatic toad will provide a solid foundation to understand the genetic basis of its many biological processes.

Background Color vision and phototactic behavior based on opsins are important for the fitness of insects because of their roles in foraging and mate choice. Related topics, including the duplication and loss of opsin genes, have been well investigated in insect orders such as Coleoptera, Lepidoptera, Hymenoptera, Odonata and Orthoptera, and the findings have been used to develop pest management strategies involving light trapping. Mirid bugs of Hemiptera, which are pests that cause heavy economic losses, show capacity for color discrimination and phototaxis. However, the opsins in mirid bugs remain uncharacterized. Herein, we examined five species to investigate the evolution of opsins in the family Miridae. Results Using RNA-seq, we identified several contigs showing high identity with opsins, including four contigs in Apolygus lucorum and three contigs each in Adelphocoris suturalis, Adelphocoris fasciaticollis, Adelphocoris lineolatus and Nesidiocoris tenuis. Phylogenetic analyses indicated that one of these genes clustered with ultraviolet-sensitive (UV) opsins and that the others clustered with long-wavelength (LW) opsins, suggesting that duplication of LW opsins and loss of blue light-sensitive (B) opsins occurred in mirid bugs. The existence of introns in the LW opsins of mirid bugs suggested that the duplication events were DNA based. Both LW1 and LW2 opsins of mirid bugs were found to be under strong purifying selection. The LW1 opsins were significantly more highly expressed than the LW2 and UV opsins. Conclusions We identified the opsins of mirid bugs using five selected mirid species as a representative sample. Phylogenetic analyses clustered one of the genes with UV opsins and the others with LW opsins, suggesting the occurrence of LW opsin duplication and B opsin loss during the evolution of mirid bugs. Intron detection suggested that the identified duplication event was DNA based. The evidence of strong purifying selection and the relatively high expression levels suggested that these opsins exhibit fundamental functions in mirid bugs.

以东海沿海捕获的野生真蛸(Octopus sinensis)为实验材料,用含秋水仙素终浓度为0.005％的海水活体暂养的方法,取鳃和肾脏细胞,利用热滴片法制备染色体标本,对其核型进行分析.结果显示,真蛸的二倍体染色体条数为60条,核型公式为2n=14 m+26 sm+12 st+8 t,其染色体臂数(NF)为100.未发现带有随体和次溢痕的染色体和异型染色体,推断真蛸可能为常染色体性别决定类型.本研究可为蛸属的细胞遗传学研究及真蛸种质鉴定和资源保护提供基础资料和参考依据.

The Cephalopoda are a group of highly diverse marine species in the phylum Mollusca, which are distributed worldwide. They have evolved some vertebrate‐like biological traits and exhibit complicated behavioural repertoires. Thus, they are interesting species for studying the mechanisms of evolutionary convergence, innovational functional structures and evolutionary adaptation to a highly active, predatory lifestyle in diverse marine environments. Despite the evolutionary placement and biological significance of cephalopods, genomic data on these organisms remain limited. Here, we assembled a chromosome‐level genome of a female East Asian common octopus (Octopus sinensis) by combining Pacific Bioscience (PacBio) single‐molecule real‐time sequencing, Illumina paired‐end sequencing and Hi‐C technology. An O. sinensis genome of 2.72 Gb was assembled from a total of 245.01 Gb high‐quality PacBio sequences. The assembled genome represents 80.2% completeness (BUSCO) with a contig N50 of 490.36 Kb and a scaffold N50 of 105.89 Mb, showing a considerable improvement compared with other sequenced cephalopod genomes. Hi‐C scaffolding of the genome resulted in the construction of 30 pseudochromosomes in Cephalopoda, representing 96.41% of the assembled sequences. The genome contained 42.26% repeat sequences and 5,245 noncoding RNAs. A total of 31,676 protein‐coding genes were predicted, of which 82.73% were functionally annotated. The comparative genomic analysis identified 17,020 orthologous gene families, including 819 unique gene families and 629 expanded gene families. This genomic information will be an important molecular resource for further investigation of biological function and evolutionary adaptations in octopuses, and facilitate research into their population genetics and comparative evolution.

Background To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species ( Bufo tibetanus , Nanorana parkeri , Rana kukunoris and Scutiger boulengeri ) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. Results Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar’s test. Then, the R conv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri , had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3–32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. Conclusions There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.

Additional file 9: Table S8. Results from enrichment analysis of convergent and parallel genes based on dataset 2–7.

The Shedao pit-viper (Gloydius shedaoensis) exhibits an extreme sedentary lifestyle. The island species exclusively feeds on migratory birds during migratory seasons and experiences prolonged hibernation and aestivation period each year (up to eight months). The sedentary strategy reduces energy expenditure, but may trigger a series of adverse effects and the snakes have likely evolved genetic modifications to alleviate these effects. To investigate the genetic adaptations, we sequenced and compared the transcriptomes of the Shedao pit-viper and its closest mainland relative, the black eyebrow pit-viper (G. intermedius). The Shedao pit-viper revealed a low rate of molecular evolution compared to its mainland relative, which is possibly associated with metabolic suppression. Signals of positive selection were detected in two genes related to antithrombin (SERPINC1) and muscle atrophy (AARS). Those genes exert significant functions in thrombosis, inhibiting oxidation and prolonged fasting. Convergent and parallel substitutions of amino acid with two other sedentary vertebrates, which often suggest adaptation, were found in a fatty acid beta-oxidation related gene (ACATA1) and a circadian link gene (KLF10), which regulate lipogenesis, gluconeogenesis, and glycolysis. Furthermore, a circadian clock gene (CRY2) exhibited two amino acid substitutions specific to the Shedao pit-viper and one variant was predicted to affect protein function. Modifications of these genes and their related functions may have contributed to the survival of this island snake species with a sedentary lifestyle and extreme seasonal food availability. Our study demonstrated several important clues for future research on physiological and other phenotypic adaptation.

BackgroudHorizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g., mirid bugs and beetles). Here, we chose three phytozoophagous mirid bugs (Adelphocoris suturalis, A. fasciaticollis, A. lineolatus) and one zoophytophagous mirid bug (Nesidiocoris tenuis) to detect whether the duplication, molecular evolution, and expression levels of PGs were related to host range expansion in mirid bugs.ResultsBy RNA-seq, we reported 30, 20, 19 and 8 PGs in A. suturalis, A. fasciaticollis, A. lineolatus and N. tenuis, respectively. Interestingly, the number of PGs was significantly positive correlation to the number of host plants (P=0.0339) in mirid bugs. Most PGs (>17) were highly expressed in the three phytozoophagous mirid bugs, while only one PG was relatively highly expressed in the zoophytophagous mirid bug. Natural selection analysis clearly showed that a significant relaxation of selection pressure acted on the PGs in zoophytophagous mirid bugs (K=0.546, P=0.0158) rather than in phytozoophagous mirid bugs (K=1, P=0.92), suggesting a function constraint of PGs in phytozoophagous mirid bugs.ConclusionTaken together with gene duplication, molecular evolution, and expression levels, our results suggest that PGs are more strictly required by phytozoophagous than by zoophytophagous mirid bugs and that the duplication of PGs is associated with the expansion of host plant ranges in mirid bugs.

The small brown planthopper (SBPH), Laodelphax striatellus, is one of the most destructive agricultural pests that causes serious economic loss in the main rice‐producing areas of China. To clarify issues such as the genetic differentiation, gene flow and population genetic structure of SBPH populations, we investigated the genetic diversity, genetic structure and phylogeography of 27 SBPH populations at 23 sampling sites from three climatic zones of China using specific‐locus amplified fragment sequencing (SLAF‐seq) for large‐scale single nucleotide polymorphism (SNP) detection. In total, 115.95 M reads, 56,355 polymorphic specific‐locus amplified fragments were developed, and 32,556 reliable single nucleotides (SNPs) were detected. The results indicated that the genotypes of many polymorphism sites had low heterozygosity in every population. Overall, the pairwise FST values between the populations varied from 0.056 to 0.092; it suggested the lack of strong differentiation among three climatic zone groups, respectively. It also suggested a strong level of gene flow (Nm) among populations in different climate zones, ranging from 28.864 to 35.197. Phylogenetic analyses, principal component analysis (PCA), Bayesian clustering method and AMOVA revealed that there was no evidence genetic clustering in three main bioclimatic zones. Neutrality testing provided strong evidence for a recent rapid expansion without any recent genetic bottleneck in these populations. Accordingly, the results of the present study should be beneficial for SBPH management and provide insight into the genetics of SBPH.

Polyploidization occurs widely in eukaryotes, and especially in plants. Polyploid plants and some fishes have been commercialized. Typically, severe genomic perturbations immediately follow polyploidization and little is known about how polyploid offspring survives the genetic and epigenetic changes. Investigations into this require the identification of genes related to polyploidization and the discrimination of dosage-balance from paternal and maternal copies, and regardless of the mechanism being either autopolyploidization or allopolyploidization. New approaches and technologies may discern the mosaic of novel gene functions gained through the recombination of paternal and maternal genes in allopolyploidization. Modifications of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) with CRISPR-associated system (Cas) protein 9 (CRISPR/Cas9) have been employed in studies of polyploidization of plants. However, the approach has seldom been applied to polyploidization in vertebrates. Herein, we use CRISPR/Cas9 to trace gene-fate in tetraploid goldfish, and specifically to identify the functional differentiation of two divergent copies of fgf20a, which are expressed differently throughout embryonic development. We expect this gene editing system will be applicable to studies of polyploids and the genetic improvement of polyploid livestock.

Quaternary climatic oscillations and geography are of primary importance in shaping intraspecific genetic diversity. We examined the diversification patterns and inferred processes for the green odorous frog ( Odorrana margaretae ) of western China. Species distribution modelling showed that the species has a continuous circular distribution around the Sichuan Basin while the basin itself is largely uninhabitable. Population genetic and phylogenetic analyses revealed that the species has a ring‐shaped divergent pattern. While the chain of populations around the Basin maintains a mostly gradual and continuous genetic variation, populations between the north and west showed little gene exchange. Two processes, glacial refugial history and geography, likely contributed to the observed patterns. Our genetic clustering analysis revealed two clusters, suggesting two refugial groups among the populations, one from the west and the other from the east. Postglacial expansion may have created two contact zones. One at the south had extensive population admixture and produced a gradual transition between the western and eastern populations. Consequently, this region has the highest genetic diversity and represents an evolutionary “melting pot.” In contrast, the second contact zone at the northwestern side of the Basin has limited admixture, suggesting partial reproductive isolation between the northern and western populations. Furthermore, an isolation‐by‐distance analysis revealed a strong correlation (Mantel r = 0.745) between the genetic and geographic distances, when we assumed that populations were connected following the circular distribution without gene flow across the NW contact zone. We also explored alternative explanations, such as a one‐refugium scenario. With its micro‐ring, the green odorous frog is poised to make an excellent model system for understanding the process of speciation.

HSP90AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90AA1 gene in high elevation amphibians. IISP90AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N parkeri and R. kukunoris. We generated both model based (Zhang and Kumar's test) and empirical data based (parallel/divergence plotting) null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported Glade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.

Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are becoming increasingly available, there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. There exists no species delimitation methods that are based on machine learning. Our method treats the species delimitation problem as a classification problem. It is a problem of identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purpose. Each pair of known populations are combined to form training samples with a label of “same species” or “different species”. We use Support Vector Machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: “same species” or “different species”. Given multi-locus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, e.g. with short species divergence time and gene flow.

BACKGROUND:Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations to high-altitude adaptation in Asiatic toads (Bufo gargarizans), we implemented a reciprocal transplant experiment between low- and high-altitude sites and sequenced 12 transcriptomes from brain, heart, and liver tissues.RESULTS:A large number of genes with expression differences (DEGs) between high- and low-altitude individuals (193 fixed and 844 plastic) were identified, and the majority of them were tissue specific. Heart displayed the largest number of DEGs, both plastic and fixed. Fixed DEGs were particularly concentrated in functions associated with muscle contraction, and the majority of them were down-regulated in high-altitude individuals. Plastic DEGs were highly concentrated in several energy metabolism related functional categories, and the majority of them were also down-regulated at high-altitude environments. In liver samples, genes associated with nutrient metabolism experienced a broad-scale expression down-regulation in high-altitude toads.CONCLUSIONS:These broadly suppressed expression patterns at high altitudes are in strong contrast to those of endothermic homeotherms, suggesting poikilothermic vertebrates may have adopted different strategies at high altitudes. Our results strongly support that both genotypic specialization and phenotypic plasticity play crucial role in adaptation to high altitude for Asiatic toads. Poikilothermic vertebrates are among the most hypoxia-tolerant animals known, and many molecular mechanisms remain elusive. We hope that our results will provide useful directions for future research.

We report a strong pattern of molecular-level convergent/parallel evolution of the MYBPC2 gene. Three high-elevation amphibian species, Bufo gargarizans minshanicus, Nanorana pleskei, Rana kukunoris, revealed remarkable numbers of convergent and parallel amino acid substitutions. On the MYBPC2 gene tree of eleven anurans, the three distantly related species formed a strongly supported clade that was away from their respective relatives. Furthermore, we generated both model-based and empirical data-based null distributions for neutral convergent evolution. All three pairwise comparisons among the three species showed significantly more convergent and parallel substitutions than the null distributions. This study adds to the very small roster of clear cases of non-neutral molecular convergent evolution (e.g. prestin, rhodopsin). Molecular convergent evolution has significant implications in biology and detailed case studies will likely provide more insight into its genetic mechanisms.

The phylogenetic relationships of Asian schilbid catfishes of the genera Clupisoma, Ailia, Horabagrus, Laides and Pseudeutropius are poorly understood, especially those of Clupisoma. Herein, we reconstruct the phylogeny of 38 species of catfishes belonging to 28 genera and 14 families using the concatenated mitochondrial genes COI, cytb, and 16S rRNA, as well as the nuclear genes RAG1 and RAG2. The resulting phylogenetic trees consistently place Clupisoma as the sister taxon of Laides, and the five representative Asian schilbid genera form two monophyletic groups with the relationships (Ailia (Laides, Clupisoma)) and (Horabagrus, Pseudeutropius). The so-called "Big Asia" lineage relates distantly to African schilbids. Independent analyses of the mitochondrial and nuclear DNA data yield differing trees for the two Asian schilbid groups. Analyses of the mitochondrial gene data support a sister-group relationship for (Ailia (Laides, Clupisoma)) and the Sisoroidea and a sister-taxon association of (Horabagrus, Pseudeutropius) and the Bagridae. In contrast, analyses of the combined nuclear data indicate (Ailia (Laides, Clupisoma)) to be the sister group to (Horabagrus, Pseudeutropius). Our results indicate that the Horabagridae, recognized by some authors as consisting of Horabagrus, Pseudeutropius and Clupisoma does not include the latter genus. We formally erect a new family, Ailiidae fam. nov. for a monophyletic Asian group comprised of the genera Ailia, Laides and Clupisoma.

Significance Why is polyploidization rarer in animals than in plants? This question remains unanswered due to the absence of a suitable system in animals for studying instantaneous polyploidization and the crucial changes that immediately follow hybridization. RNA-seq analyses discover extensive chimeric genes and immediate mutations of orthologs in both diploid and tetraploid offspring of the goldfish (♀) × common carp (♂) hybrids. Overall, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. Some chimeric and differentially expressed genes relate to crucial functions of normal cell cycle activities, and cancer-related pathways in 2nF 1 . The discovery of fast changes at the levels of chromosomes, genomic DNA, and transcriptomes suggests that allopolyploidization hinders genomic functions in vertebrates, and this conclusion may extend to all animals.