Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans.

BACKGROUND: Cetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory systems. This process of evolution has resulted in the emergence of distinctive phenotypic traits, notably the abundance of elastic fibers and thickened alveolar walls in their lungs, which may facilitate alveolar collapse during diving. This structure helps selective exchange of oxygen and carbon dioxide, while minimizing nitrogen exchange, thereby reducing the risk of DCS. Nevertheless, the scientific inquiry into the mechanisms through which these unique phenotypic characteristics govern the diving behavior of marine mammals, including cetaceans, remains unresolved. RESULTS: This study entails an evolutionary analysis of 42 genes associated with pulmonary fibrosis across 45 mammalian species. Twenty-one genes in cetaceans exhibited accelerated evolution, featuring specific amino acid substitutions in 14 of them. Primarily linked to the development of the respiratory system and lung morphological construction, these genes play a crucial role. Moreover, among marine mammals, we identified eight genes undergoing positive selection, and the evolutionary rates of three genes significantly correlated with diving depth. Specifically, the SFTPC gene exhibited convergent amino acid substitutions. Through in vitro cellular experiments, we illustrated that convergent amino acid site mutations in SFTPC contribute positively to pulmonary fibrosis in marine mammals, and the presence of this phenotype can induce deep alveolar collapse during diving, thereby reducing the risk of DCS during diving. CONCLUSIONS: The study unveils pivotal genetic signals in cetaceans and other marine mammals, arising through evolution. These genetic signals may influence lung characteristics in marine mammals and have been linked to a reduced risk of developing DCS. Moreover, the research serves as a valuable reference for delving deeper into human diving physiology.

Diversified Mammalian Visuasl Adaptations to Bright- or Dim-Light Environments.

Photic niche shifts of mammals are associated with changing visual capabilities, primarily mediated by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin (RH1) for dim-light vision. To further elucidate molecular mechanisms of mammalian visual adaptations to different light environments, a systematic study incorporating evolutionary analyses across diverse groups and in vitro assays have been carried out. Here, we collected gene sequences for the three opsins from 220 species covering all major mammalian clades. After screening for cone opsin gene losses, we estimated selective pressures on each of the three genes and compared the levels of selection experienced by species living in bright- and dim-light environments. SWS1 pigment is shown to experience accelerated evolution in species living in bright-light environments as has RH1 in aquatic cetaceans, indicating potential shifts for ecological adaptations. To further elucidate the functional mechanisms for these two pigments, we then carried out site-directed mutagenesis in representative taxa. For SWS1, violet and ultraviolet sensitivities in the pika and mouse are mainly affected by substitutions at the critical sites 86 and 93, which have strong epistatic interaction. For RH1, the phenotypic difference between the sperm whale and bovine sequences is largely contributed by a substitution at site 195, which could be critical for dim-light sensation for deep-diving species. Different evolutionary patterns for the visual pigments have been identified in mammals, which correspond to photic niches, although additional phenotypic assays are still required to fully explain the functional mechanisms.

Esketamine pretreatment during cesarean section reduced the incidence of postpartum depression: a randomized controlled trail.

BACKGROUND: Postpartum depression (PPD) is a common mental disease in postpartum women, which has received more and more attention in society. Ketamine has been confirmed for its rapid antidepressant effect in women with PPD. We speculate that esketamine, an enantiomer of ketamine, pretreatment during cesarean can also reduce the incidence of PPD. METHODS: All the parturients enrolled in the study were randomly assigned to two groups: the esktamine group (0.2 mg/kg esketamine) and the control group (a same volume of saline). All the drugs were pumped for 40 min started from the beginning of the surgery. The Amsterdam Anxiety and Information Scale (APAIS) scores before the surgery, the Edinburgh postnatal depression scale (EPDS) scores at 4 d and 42 d after surgery, the Pain Numerical Rating Scale (NRS) scores at 6 h, 12 h, 24 h and 48 h post-operation were evaluated, as well as the adverse reactions were recorded. RESULTS: A total of 319 parturients were analyzed in the study. The incidence of PPD (EPDS score > 9) in the esketamine group was lower than the control group at 4 days after surgery (13.8% vs 23.1%, P = 0.0430) but not 42 days after surgery (P = 0.0987). Esketamine 0.2 mg/kg could reduce the NRS score at 6 h,12 h and 24 h after surgery, as well as the use of vasoactive drugs during surgery (P < 0.05). The incidences of maternal dizziness (17.0%), blurred vision (5%), illusion (3.8%) and drowsiness (3.8%) in the esketamine group were higher than those of control group (P < 0.05). CONCLUSIONS: Intraoperative injection of esketamine (0.2 mg/kg) prevented the occurrence of depression (EPDS score > 9) at 4 days after delivery but not 42 days. Esketamine reduced the NRS scores at 6 h, 12 h and 24 h after surgery, but the occurrence of maternal side effects such as dizziness, blurred vision, drowsiness and hallucination were increased. TRIAL REGISTRATION: Registered in the Chinese Clinical Trial Registry (ChiCTR2100053422) on 20/11/2021.

Evolutionary analysis of the mTOR pathway provide insights into lifespan extension across mammals.

BACKGROUND: Lifespan extension has independently evolved several times during mammalian evolution, leading to the emergence of a group of long-lived animals. Though mammalian/mechanistic target of rapamycin (mTOR) signaling pathway is shown as a central regulator of lifespan and aging, the underlying influence of mTOR pathway on the evolution of lifespan in mammals is not well understood. RESULTS: Here, we performed evolution analyses of 72 genes involved in the mTOR network across 48 mammals to explore the underlying mechanism of lifespan extension. We identified a total of 20 genes with significant evolution signals unique to long-lived species, including 12 positively selected genes, four convergent evolution genes, and five longevity associated genes whose evolution rate related to the maximum lifespan (MLS). Of these genes, four positively selected genes, two convergent evolution genes and one longevity-associated gene were involved in the autophagy response and aging-related diseases, while eight genes were known as cancer genes, indicating the long-lived species might have evolved effective regulation mechanisms of autophagy and cancer to extend lifespan. CONCLUSION: Our study revealed genes with significant evolutionary signals unique to long-lived species, which provided new insight into the lifespan extension of mammals and might bring new strategies to extend human lifespan.

Functional Attenuation of UCP1 as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans.

Uncoupling protein 1 (UCP1) is an essential protein in the mitochondrial inner membrane that mediates nonshivering thermogenesis (NST) and plays an important role in thermoregulation and fat deposition. However, the relationship between the evolution of UCP1 and fat deposition in the blubber layer in cetaceans remains unclear. Here, frameshift mutations, premature termination, and relaxed selection pressure (ω = 0.9557, P < 0.05) were detected in UCP1 in cetaceans, suggesting that UCP1 was inactivated during cetacean evolution. By time estimation, it was found that the inactivation of UCP1 in cetaceans occurred between 53.1 and 50.2 Ma. However, combined with findings from immunohistochemical analysis of the blubber layer of the Yangtze finless porpoise and in vitro functional assays, a premature termination of cetacean UCP1 resulted in a reduction of UCP1-mediated NST capacity (about 50%) and lipolytic capacity (about 40%), both of which were beneficial to maintain blubber layer and body temperature without excessive fat consumption. This study provides new insights into the molecular mechanisms of the blubber thickening in cetaceans and highlights the importance of UCP1 attenuation in cetaceans for secondary aquatic adaptation.

Divergence of Tbx4 hindlimb enhancer HLEA underlies the hindlimb loss during cetacean evolution.

The cetacean hindlimb skeleton massively decreased to only vestigial limb elements as cetaceans evolved from land to aquatic lifestyles; however, the molecular mechanism underlying this major morphological transition remains unclear. In this study, four deletions and specific substitutions were detected in cetacean hindlimb enhancer A (HLEA), an enhancer that can regulate Tbx4 expression in hindlimb tissues to control hindlimb development. Transcriptional activation of HLEA was significantly weaker in bottlenose dolphin than mice, and this was found to be closely associated with cetacean-specific deletions. Furthermore, deletions in cetacean HLEA might disrupt HOX and PITX1 binding sites, which are required for enhancer activation. The ancestral state of these deletions was investigated, and all four specific deletions were found to have occurred after the species diverged from their common ancestor, suggesting that the deletion occurred recently, during a secondary aquatic adaptation. Taking these findings together, we suggest that cetacean-specific sequence changes reduced the Tbx4 gene expression pattern, and consequently drove the gradual loss of hindlimb in cetaceans.

Evolutionary genetics of flipper forelimb and hindlimb loss from limb development-related genes in cetaceans.

BACKGROUND: Cetacean hindlimbs were lost and their forelimb changed into flippers characterized by webbed digits and hyperphalangy, thus allowing them to adapt to a completely aquatic environment. However, the underlying molecular mechanism behind cetacean limb development remains poorly understood. RESULTS: In the present study, we explored the evolution of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with that of other mammals. TBX5, a forelimb specific expression gene, was identified to have been under accelerated evolution in the ancestral branches of cetaceans. In addition, 32 cetacean-specific changes were examined in the SHH signaling network (SHH, PTCH1, TBX5, BMPs and SMO), within which mutations could yield webbed digits or an additional phalange. These findings thus suggest that the SHH signaling network regulates cetacean flipper formation. By contrast, the regulatory activity of the SHH gene enhancer-ZRS in cetaceans-was significantly lower than in mice, which is consistent with the cessation of SHH gene expression in the hindlimb bud during cetacean embryonic development. It was suggested that the decreased SHH activity regulated by enhancer ZRS might be one of the reasons for hindlimb degeneration in cetaceans. Interestingly, a parallel / convergent site (D42G) and a rapidly evolving CNE were identified in marine mammals in FGF10 and GREM1, respectively, and shown to be essential to restrict limb bud size; this is molecular evidence explaining the convergence of flipper-forelimb and shortening or degeneration of hindlimbs in marine mammals. CONCLUSIONS: We did evolutionary analyses of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with those of other mammals to provide novel insights into the molecular basis of flipper forelimb and hindlimb loss in cetaceans.

Gene Duplication and Loss of AANAT in Mammals Driven by Rhythmic Adaptations.

Arylalkylamine N-acetyltransferase (AANAT) plays a crucial role in synchronizing internal biological functions to circadian and circannual changes. Generally speaking, only one copy of AANAT gene has been found in mammals, however, three independent duplications of this gene were detected in several cetartiodactyl lineages (i.e., Suidae, Hippopotamidae, and Pecora), which originated in the middle Eocene, a geological period characterized with the increased climate seasonality. Lineage-specific expansions of AANAT and the associated functional enhancement in these lineages strongly suggest an improvement in regulating photoperiodic response to adapt to seasonal climate changes. In contrast, independent inactivating mutations or deletions of the AANAT locus were identified in the four pineal-deficient clades (cetaceans, sirenians, xenarthrans, and pangolins). Loss of AANAT function in cetaceans and sirenians could disrupt the sleep-promoting effects of pineal melatonin, which might contribute to increasing wakefulness, adapting these clades to underwater sleep. The absence of AANAT and pineal glands in xenarthrans and pangolins may be associated with their body temperature maintenance. The present work demonstrates a far more complex and intriguing evolutionary pattern and functional diversity of mammalian AANAT genes than previously thought and provides further evidence for understanding AANAT evolution as driven by rhythmic adaptations in mammals.

Over-expression of the bottlenose dolphin Hoxd13 gene in zebrafish provides new insights into the cetacean flipper formation.

Cetaceans have evolved elongated soft-tissue flipper with digits made of hyperphalangy. Cetaceans were found to have 2-3 more alanine residues in Hoxd13 than other mammals, which were suggested to be related to their flipper. However, how Hoxd13 regulates other genes and induces hyperphalangy in cetaceans remain poorly understood. Here, we overexpressed the bottlenose dolphin Hoxd13 in zebrafish (Danio rerio). Combined with transcriptome data and evolutionary analyses, our results revealed that the Wingless/Integrated (Wnt) and Hedgehog signaling pathways and multiple genes might regulate hyperphalangy development in cetaceans. Meanwhile, the Notch and mitogen-activated protein kinase (Mapk) signaling pathways and Fibroblast growth factor receptor 1 (Fgfr1) are probably correlated with interdigital tissues retained in the cetacean flipper. In conclusion, this is the first study to use a transgenic zebrafish to explore the molecular evolution of Hoxd13 in cetaceans, and it provides new insights into cetacean flipper formation.

Genomic insights into body size evolution in Carnivora support Peto's paradox.

BACKGROUND: The range of body sizes in Carnivora is unparalleled in any other mammalian order-the heaviest species is 130,000 times heavier than the lightest and the longest species is 50 times longer than the shortest. However, the molecular mechanisms underlying these huge differences in body size have not been explored. RESULTS: Herein, we performed a comparative genomics analysis of 20 carnivores to explore the evolutionary basis of the order's great variations in body size. Phylogenetic generalized least squares (PGLS) revealed that 337 genes were significantly related to both head body length and body mass; these genes were defined as body size associated genes (BSAGs). Fourteen positively-related BSAGs were found to be associated with obesity, and three of these were under rapid evolution in the extremely large carnivores, suggesting that these obesity-related BSAGs might have driven the body size expansion in carnivores. Interestingly, 100 BSAGs were statistically significantly enriched in cancer control in carnivores, and 15 of which were found to be under rapid evolution in extremely large carnivores. These results suggested that large carnivores might have evolved an effective mechanism to resist cancer, which could be regarded as molecular evidence to support Peto's paradox. For small carnivores, we identified 15 rapidly evolving genes and found six genes with fixed amino acid changes that were reported to reduce body size. CONCLUSIONS: This study brings new insights into the molecular mechanisms that drove the diversifying evolution of body size in carnivores, and provides new target genes for exploring the mysteries of body size evolution in mammals.

Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals.

BACKGROUND: Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. RESULTS: In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. CONCLUSIONS: Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the "cooling hypothesis", which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the "training hypothesis", which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.

CP-25 alleviates antigen-induced experimental Sjögren's syndrome in mice by inhibiting JAK1-STAT1/2-CXCL13 signaling and interfering with B-cell migration.

The etiology of primary Sjögren's syndrome (pSS) remains unknown, and there is no complete curative drug. In this study, we treated a mouse model of the submandibular gland (SG) protein-immunized experimental Sjögren's syndrome (ESS) with paeoniflorin-6'-O-benzene sulfonate (termed CP-25) to evaluate the potential therapeutic effects of CP-25. Through in vivo experiments, we found that CP-25 increased saliva flow, alleviated the salivary gland indexes, and improved tissue integrity in the ESS model. The viability of splenocytes and B-lymphocyte migration from spleen were reduced in ESS mice. Furthermore, CP-25 decreased the expression of IgG antibodies, anti-SSA and anti-SSB antibodies and modulated the levels of cytokines in the serum of SS mice. The numbers of total B lymphocytes, plasma cells (PCs), and memory B cells diminished in the salivary gland. Increased expression of the JAK1-STAT1-CXCL13 axis and IFNα was found in human tissue isolated from pSS patients. In vitro, after stimulation with IFNα, the levels of CXCL13 mRNA and CXCL13 in human salivary gland epithelial cells (HSGEC) increased, while CP-25 counteracted the secretion of CXCL13 and downregulated the expression of CXCL13. IFN-α activated the JAK1-STAT1/2-CXCL13 signaling pathway in HSGEC, which was negatively regulated by additional CP-25. As a consequence, B-cell migration was downregulated in coculture with IFN-α-stimulated HSGEC. Taken together, this study demonstrated that the therapeutic effects of CP-25 were associated with the inhibition of the JAK1-STAT1/2-CXCL13 signaling pathway in HSGEC, which impedes the migration of B cells into the salivary gland. We identified the underlying mechanisms of the therapeutic effect of CP-25 and provided an experimental foundation for CP-25 as a potential drug in the treatment of the human autoimmune disorder pSS.

Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals.

Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.

Insights into Dietary Switch in Cetaceans: Evidence from Molecular Evolution of Proteinases and Lipases.

Fossil evidence suggests that cetaceans evolved from artiodactylans. Thus, there was a major dietary change from herbivorous to carnivorous during their transition from a terrestrial to an aquatic environment. However, the molecular evolutionary mechanisms underlying this dietary switch have not been well investigated. Evidence of positive selection of digestive proteinases and lipases of cetaceans was detected: (1) For the four pancreatic proteinase families (carboxypeptidase, trypsin, chymotrypsin, and elastase) examined in this study, each family included only a single intact gene (e.g., CPA1, PRSS1, CTRC, and CELA3B) that had no ORF-disrupted or premature stop codons, whereas other members of each family had become pseudogenized. Further selective pressure analysis showed that three genes (PRSS1, CTRC, and CELA3B) were subjected to significant positive selection in cetaceans. (2) For digestive proteinases from the stomach, PGA was identified to be under positive selection. (3) Intense positive selection was also detected for the lipase gene PLRP2 in cetaceans. In addition, parallel /convergent amino acid substitutions between cetaceans and carnivores, two groups of mammals that have evolved similar feeding habits, were identified in 10 of the 12 functional genes. Although pseudogenization resulted in each family of pancreatic proteinases only retaining one intact gene copy in cetacean genomes, positive selection might have driven pancreatic proteinases, stomach proteinases, and lipases to adaptively evolve a stronger ability to digest a relatively higher proportion of proteins and lipids from animal foods. This study can provide some novel insights into the molecular mechanism of cetacean dietary changes during their transition from land to sea.

Accelerated evolution and diversifying selection drove the adaptation of cetacean bone microstructure.

BACKGROUND: The transition from land to sea by the ancestor of cetaceans approximately 50 million years ago was an incredible evolutionary event that led to a series of morphological, physiological, and behavioral adaptations. During this transition, bone microstructure evolved from the typical terrestrial form to the specialized structure found in modern cetaceans. While the bone microstructure of mammals has been documented before, investigations of its genetic basis lag behind. The increasing number of cetaceans with whole-genome sequences available may shed light on the mechanism underlying bone microstructure evolution as a result of land to water transitions. RESULTS: Cetacean bone microstructure is consistent with their diverse ecological behaviors. Molecular evolution was assessed by correlating bone microstructure and gene substitution rates in terrestrial and aquatic species, and by detecting genes under positive selection along ancestral branches of cetaceans. We found that: 1) Genes involved in osteoclast function are under accelerated evolution in cetaceans, suggestive of important roles in bone remodeling during the adaptation to an aquatic environment; 2) Genes in the Wnt pathway critical for bone development and homeostasis show evidence of divergent evolution in cetaceans; 3) Several genes encoding bone collagens are under selective pressure in cetaceans. CONCLUSIONS: Our results suggest that evolutionary pressures have shaped the bone microstructure of cetaceans, to facilitate life in diverse aquatic environments.

Insights into body size variation in cetaceans from the evolution of body-size-related genes.

BACKGROUND: Cetaceans exhibit an exceptionally wide range of body size, yet in this regard, their genetic basis remains poorly explored. In this study, 20 body-size-related genes for which duplication, mutation, or deficiency can cause body size change in mammals were chosen to preliminarily investigate the evolutionary mechanisms underlying the dramatic body size variation in cetaceans. RESULTS: We successfully sequenced 20 body-size-related genes in six representative species of cetaceans. A total of 46 codons from 10 genes were detected and determined to be under strong positive selection, 32 (69.6%) of which were further found to be under radical physiochemical changes; moreover, some of these sites were localized in or near important functional regions. Interestingly, positively selected genes were well matched with body size evolution: for small cetaceans, strong evidence of positive selection was detected at ACAN, OBSL1, and GRB10, within which mutations or duplications could cause short stature; positive selection was found in large cetaceans at CBS and EIF2AK3, which could promote growth, and at the PLOD1 gene, within which mutations could cause tall stature. Importantly, relationship analyses revealed that the evolutionary rate of CBS was positively related to body length and body mass with statistical significance. Additionally, we identified 32 cetacean-specific amino acid changes in 10 genes. CONCLUSIONS: This is the first study to investigate the molecular basis of dramatic body size variation in cetaceans. Our results provide evidence of the positive selection of several body-size-related genes in cetaceans, as well as divergent selection between large or small cetaceans, which suggest cetacean body size variation possibly associated with these genes. In addition, cetacean-specific amino acid changes might have played key roles in body size evolution after the divergence of cetaceans from their terrestrial relatives. Overall, the evolutionary pattern of these body-size-related genes could provide new insights into genetic mechanisms for the body size variation in cetaceans.

Genomic Organization and Phylogeny of MHC Class II Loci in Cetaceans.

Cetaceans are a suborder of secondarily adapted aquatic mammals with an enigmatic history involving a transition from land to sea approximately 55 Mya. During the transition period, cetaceans would have faced many new pathogen challenges, but limited information is available about the adaptive immune system of these mammals. The major histocompatibility complex (MHC) family plays a key role in antigen recognition and presentation in adaptive immunity, which is believed to have evolved in response to pathogens. In the present study, MHC class II loci were characterized in 7 published cetacean genome assemblies and the genomic organization of cetaceans was compared with that of their terrestrial relatives, the cow, sheep, and pig. A total of 9 MHC class II loci were identified in the cetacean genomes: DRA, DRB, DQA, DQB, DPB, DOA, DOB, DMA, and DMB. Sequences from 8 of the 9 genes included intact coding regions and were presumably functional. The organization of the MHC class II loci was conserved across the examined mammalian species, whereas the orientation and number of the alpha and beta genes varied among the species. The phylogenetic reconstruction of all MHC genes from Cetartiodactyla suggested that alpha and beta genes had different topologies. Additionally, based on a phylogenetic reconstruction of the multi-locus DRB, 2 (DRB1 and DRB2) of the 4 putative gene copies were hypothesized to have duplicated and evolved during the radiation of cetaceans.

Molecular cloning and expression pattern of IGFBP-2a in black porgy (Acanthopagrus schlegelii) and evolutionary analysis of IGFBP-2s in the species of Perciformes.

Insulin-like growth factor-binding protein-2 (IGFBP-2) plays a key role in regulating growth and development by its affinity with insulin-like growth factors (IGFs). In this study, we cloned the coding sequence (CDS) of IGFBP-2a from the black porgy (Acanthopagrus schlegelii) muscle and identified that the full-length CDS of IGFBP-2a was 882 bp. Real-time quantitative PCR revealed that IGFBP-2a was most abundant in the liver of the black porgy and backcross breed (F1♀×black porgy♂) but remained lower in each tested tissue in self-cross breed (F1♀×F1♂). In addition, the IGFBP-2a expression in the liver of three breeds showed a negative correlation with their growth rates, indicating that the IGFBP-2a played a growth-inhibiting role in the three breeds. We further identified 810 bp IGFBP-2b gene from the draft genome of black porgy. Finally, we examined the IGFBP-2a and IGFBP-2b genes by scanning the genomes of the species of Perciformes and found the IGFBP-2 gene duplication took place earlier than the divergence of perciform species. Interestingly, six positively selected sites were detected in both Perciformes IGFBP-2 genes, although both genes were identified to be under purifying selection. Specially, these positively selected sites were located in the functional domains, suggesting these sites played key roles in the growth of Perciformes. Our study partially explains the molecular basis for the prepotency in black porgy hybrids, which will provide guidance for their cultivation in the future.

Divergent Selection of Pattern Recognition Receptors in Mammals with Different Ecological Characteristics.

Pattern recognition receptors (PRRs) are specialized receptors that represent a key component of the host innate immune system. Whether molecular evolutionary history of different PRR classes have involved different genetic mechanisms underlying diverse pathogen environment in mammals, and whether distinct ecology of mammals may have imposed divergent selective pressures on the evolution of the PRRs, remained unknown. To test these hypotheses, we investigated the characterization of 20 genes belonging to four PRR classes in mammals. Evidence of positive selection was found in most (17 of 20) PRR genes examined, and most positively selected sites (84%) undergoing radical changes were found to fall in important functional regions, consistent with the co-evolutionary dynamics between the hosts and their microbial counterparts. We found different evolutionary patterns in different PRR classes, with the highest level of positive selection in C-type lectin receptor (CLR) family, suggesting that the capability of CLRs in response to a wide variety of ligands might explain their malleability to selection pressures. Tests using branch models that partitioned the data along habitat and social behavior found significant evidence of divergent selective pressures of PRRs among mammalian groups. Interestingly, species-specific evolution was detected on RIG-I-like helicase genes (RLRs) in cetaceans, suggesting that RLRs might play a critical role in the defense against widespread marine RNA viruses during their divergence and radiation into marine habitats. This study provides a comprehensive look at the evolutionary patterns and implications of mammalian PRRs, and highlights the importance of ecological influences in molecular adaptation.

Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes.

BACKGROUND: Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in size regulation during brain development were investigated in representative cetacean lineages. RESULTS: Sequences of MCPH2-7 genes were intact in cetaceans but frameshift mutations and stop codons was identified in MCPH1. Extensive positive selection was identified in four of six intact MCPH genes: WDR62, CDK5RAP2, CEP152, and ASPM. Specially, positive selection at CDK5RAP2 and ASPM were examined along lineages of odontocetes with increased encephalization quotients (EQ) and mysticetes with reduced EQ but at WDR62 only found along odontocete lineages. Interestingly, a positive association between evolutionary rate (ω) and EQ was identified for CDK5RAP2 and ASPM. Furthermore, we tested the binding affinities between Calmodulin (CaM) and ASPM IQ motif in cetaceans because only CaM combined with IQ, can ASPM perform the function in determining brain size. Preliminary function assay showed binding affinities between CaM and IQ motif of the odontocetes with increased EQ was stronger than for the mysticetes with decreased EQ. In addition, evolution rate of ASPM and CDK5RAP2 were significantly related to mean group size (as one measure of social complexity). CONCLUSIONS: Our study investigated the genetic basis of cetacean brain size evolution. Significant positive selection was examined along lineages with both increased and decreased EQ at CDK5RAP2 and ASPM, which is well matched with cetacean complex brain size evolution. Evolutionary rate of CDK5RAP2 and ASPM were significantly related to EQ, suggesting that these two genes may have contributed to EQ expansion in cetaceans. This suggestion was further indicated by our preliminary function test that ASPM might be mainly linked to evolutionary increases in EQ. Most strikingly, our results suggested that cetaceans evolved large brains to manage complex social systems, consisting with the 'social brain hypothesis', as evolutionary rate of ASPM and CDK5RAP2 were significantly related to mean group size.