Evolution of Functional Genes in Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level

Cetaceans represent an evolutionary lineage marked by drastic morphological and physiological changes during their adaptation to an exclusively marine existence. In addition, several cetacean species exhibit geographical ranges that encompass different marine environments, with genetic breaks being sometimes consistent with environmental breaks. As such, genes that underwent adaptation during the land-sea transition can also be potential candidates for adaptation to different oceanic environments. In this study, we analysed 3 milk protein genes (β-casein, κ-casein, and α-lactalbumin) and 2 immunity related genes (MHC DQβ1 and γ-fibrinogen) for selection based on available phylogenetic datasets of both mammals and cetaceans, and used the results from this analysis to assess adaptation to different environments on a population level in the European common dolphin (Delphinus delphis). We found that evidence for positive selection could be detected in all genes in the phylogenetic analyses, with β-casein showing a further increase in selective pressure in the cetacean lineage. At the population level, both the immune system locus DQβ1 and β-casein genes showed patterns of variation consistent with divergent selection, and in each case the same populations showed differentiation. One of these populations was also differentiated at neutral markers, while the other was not. We discuss possible inference, and the potential for the further development of these ideas using genomic technologies.     

Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains.     

Accelerated Evolutionary Rate of the Myoglobin Gene in Long-Diving Whales

Cetaceans, early in their evolutionary history, had developed many physiological adaptations to secondarily return to the sea. Among these adaptations, changes in molecules that transport oxygen and that ultimately support large periods of acute tissue hypoxia probably represent one big step toward the conquest of aquatic environments. Myoglobin contributes to intracellular oxygen storage and transcellular diffusion of oxygen in muscle, and plays an important role in supplying oxygen in hypoxic or ischemic conditions. Here we looked for evidence of adaptive molecular evolution of myoglobin in the cetacean lineage, relative to their terrestrial counterparts. We performed a comparative analysis to examine the variation of the parameter ω (d _N/d _S) and infer past period of adaptive evolution during the cetacean transition from the terrestrial to the aquatic environment. We also analyzed the changes in amino acid properties. At the nucleotide level, the results showed significant differences in selective pressure between cetacean and non-cetacean myoglobin (ω value three times higher in cetaceans when compared to terrestrial mammals), and also among cetacean lineages according to their diving capacities. Interestingly, both families with long duration diving cetaceans present two parallel substitutions (on sites 4 and 12). Regarding the amino acid properties, our analysis identified four significant physicochemical amino acid changes among residues in myoglobin protein under positive destabilizing selection.     

Molecular footprints of inshore aquatic adaptation in Indo-Pacific humpback dolphin (Sousa chinensis)

The Indo-Pacific humpback dolphin, Sousa chinensis, being a member of cetaceans, had fully adapted to inshore waters. As a threatened marine mammal, little molecular information available for understanding the genetic basis of ecological adaptation. We firstly sequenced and obtained the draft genome map of S. chinensis. Phylogenetic analysis in this study, based on the single copy orthologous genes of the draft genome, is consistent with traditional phylogenetic classification. The comparative genomic analysis indicated that S. chinensis had 494 species-specific gene families, which involved immune, DNA repair and sensory systems associated with the potential adaption mechanism. We also identified the expansion and positive selection genes in S. chinensis lineage to investigate the potential adaptation mechanism. Our study provided the potential insight into the molecular bases of ecological adaptation in Indo-Pacific humpback dolphin and will be also valuable for future understanding the ecological adaptation and evolution of cetaceans at the genomic level.     

Natural selection on functional modules, a genome-wide analysis

Classically, the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes. The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation. This approach, which assumed independence among genes, has not been able to identify biological functions significantly enriched in positively selected genes in individual species. Alternatively, pooling related species has enhanced the search for signatures of selection. However, grouping signatures does not allow testing for adaptive differences between species. Here we introduce the Gene-Set Selection Analysis (GSSA), a new genome-wide approach to test for evidences of natural selection on functional modules. GSSA is able to detect lineage specific evolutionary rate changes in a notable number of functional modules. For example, in nine mammal and Drosophilae genomes GSSA identifies hundreds of functional modules with significant associations to high and low rates of evolution. Many of the detected functional modules with high evolutionary rates have been previously identified as biological functions under positive selection. Notably, GSSA identifies conserved functional modules with many positively selected genes, which questions whether they are exclusively selected for fitting genomes to environmental changes. Our results agree with previous studies suggesting that adaptation requires positive selection, but not every mutation under positive selection contributes to the adaptive dynamical process of the evolution of species.     

Identification of local selective sweeps in human populations since the exodus from Africa

Selection on the human genome has been studied using comparative genomics and SNP architecture in the lineage leading to modern humans. In connection with the African exodus and colonization of other continents, human populations have adapted to a range of different environmental conditions. Using a new method that jointly analyses haplotype block length and allele frequency variation (F(ST)) within and between populations, we have identified chromosomal regions that are candidates for having been affected by local selection. Based on 1.6 million SNPs typed in 71 individuals of African American, European American and Han Chinese descent, we have identified a number of genes and non-coding regions that are candidates for having been subjected to local positive selection during the last 100 000 years. Among these genes are those involved in skin pigmentation (SLC24A5) and diet adaptation (LCT). The list of genes implicated in these local selective sweeps overlap partly with those implicated in other studies of human populations using other methods, but show little overlap with those postulated to have been under selection in the 5-7 myr since the divergence of the ancestors of human and chimpanzee. Our analysis provides focal points in the genome for detailed studies of evolutionary events that have shaped human populations as they explored different regions of the world.     

鲸类视觉退化分子机制的研究：基于GNAT2和CNGB3基因的进化分析

鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53~56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525 ~1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。     

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude.     

Candidate genes for adaptation to an aquatic habitat recovered from Ranunculus bungei and Ranunculus sceleratus

The molecular mechanisms responsible for plant adaptations to aquatic habitats remain poorly known. In this study, we aimed to detect selection on orthologous genes among the submerged aquatic plant Ranunculus bungei, semi-aquatic R. sceleratus, and terrestrial R. brotherusii and R. cantoniensis, in order to identify candidate genes involved in the adaptive transition from terrestrial habitats to aquatic habitats and if they differ between R. bungei and R. sceleratus. We used 884 previously reported 1:1:1:1 orthologous genes among the four species (one ortholog is represented in each species). We identified 177 genes of R. bungei and R. sceleratus that are potentially under positive selection. Among them, a set of candidate genes for adaptation to an aquatic habitat were recognized. These include several genes that are associated with photosynthesis, vacuoles, ethylene and oxygen receptors, and aerenchyma formation. Gene Ontology analyses suggest that the submerged R. bungei has a higher percentage of positively selected genes associated with the chloroplast and other plastids, while the semi-aquatic R. sceleratus has a higher percentage associated with metabolic processes. This study represents a step forward towards understanding the molecular mechanism of plant adaptations to aquatic habitats.     

PCR 扩增Sry 基因进行鲸类动物性别的鉴定

哺乳动物Y染色体短臂上的Sry 基因决定雄性发育方向。本研究参照哺乳动物Sry 基因保守区序列设计引物, 以非性别特异性的线粒体DNA 细胞色素b 基因作为阳性对照, 用PCR 扩增江豚、长喙真海豚等鲸类动物的Sry 基因片断并对其进行凝胶电泳分析来鉴定鲸类动物的性别。通过此方法对87 个已知性别鲸类动物标本的检验, 结果完全正确, 并进一步应用此方法成功地完成了另外33 个未知性别鲸类标本的性别鉴定。由此建立了一套简单、快速、可靠的鲸类动物的性别鉴定方法。     

鲸类低氧耐受的分子机制初探:基于HIF1α和TSC1基因的生物信息学分析

鲸类（Cetacea）具有超强潜水能力,长时间潜水造成的体内低氧是其适应完全水生生活面临的挑战之一。为了克服体内低氧环境,鲸类产生了一系列低氧耐受相关的解剖和生理等方面的适应特征,然而这一适应的分子机制仍不清楚。本研究选择在细胞感知和适应内环境氧分压变化的过程中发挥重要作用的低氧诱导因子（Hypoxia-inducible factor 1α,HIF1α）和低氧环境下抑制能量代谢的结节性复合物1（Tuberous sclerosis complex 1,TSC1）基因为候选基因,选择压力检测发现鲸类TSC1基因的6个正选择位点至少被两种最大似然法（Maximum Likelihood,ML）检测到,且通过与陆生哺乳动物同源序列比较分析,鲸类鉴定出7个特异的氨基酸突变。这些正选择和特异突变位点有30.77%（4/13）发生了激进氨基酸性质改变,且正选择位点位于重要结构域附近。正选择信号主要集中在鲸类内部各支系中,提示鲸类为了适应低氧环境,这两个基因可能发生了功能改变,以保护细胞免受低氧损伤。我们在低氧耐受不同类群间共检测到66个平行/趋同进化位点,为低氧耐受不同类群的趋同的低氧适应提供了分子证据。     

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata,Say)

Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high‐quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein‐coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein‐coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.     

鲸类二次水生生境适应Epac1和Epac2基因的分子进化

心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白（Epac1 和Epac2）基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸（Physeter macrocephalus）组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰（θ=0.5296 ± 0.1300;P<0.001）。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸（Balaena mysticetus）中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1和Epac2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。     

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality,local adaptation and demographic history

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.     

Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup

Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47 candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more prominent in chimpanzee than in human. We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans.     

Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe

The brains of odontocetes (toothed whales) look grossly different from their terrestrial relatives. Because of their adaptation to the aquatic environment and their reliance on echolocation, the odontocetes'' auditory system is both unique and crucial to their survival. Yet, scant data exist about the functional organization of the cetacean auditory system. A predominant hypothesis is that the primary auditory cortex lies in the suprasylvian gyrus along the vertex of the hemispheres, with this position induced by expansion of ‘associative′ regions in lateral and caudal directions. However, the precise location of the auditory cortex and its connections are still unknown. Here, we used a novel diffusion tensor imaging (DTI) sequence in archival post-mortem brains of a common dolphin (Delphinus delphis) and a pantropical dolphin (Stenella attenuata) to map their sensory and motor systems. Using thalamic parcellation based on traditionally defined regions for the primary visual (V1) and auditory cortex (A1), we found distinct regions of the thalamus connected to V1 and A1. But in addition to suprasylvian-A1, we report here, for the first time, the auditory cortex also exists in the temporal lobe, in a region near cetacean-A2 and possibly analogous to the primary auditory cortex in related terrestrial mammals (Artiodactyla). Using probabilistic tract tracing, we found a direct pathway from the inferior colliculus to the medial geniculate nucleus to the temporal lobe near the sylvian fissure. Our results demonstrate the feasibility of post-mortem DTI in archival specimens to answer basic questions in comparative neurobiology in a way that has not previously been possible and shows a link between the cetacean auditory system and those of terrestrial mammals. Given that fresh cetacean specimens are relatively rare, the ability to measure connectivity in archival specimens opens up a plethora of possibilities for investigating neuroanatomy in cetaceans and other species.     

A genome-wide identification of genes potentially associated with host specificity of <Emphasis Type="Italic">Brucella</Emphasis> species

Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.     

De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.     

Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

ABSTRACT: BACKGROUND: Cancer, much like most human disease, is routinely studied by utilizing model organisms. Of these model organisms, mice are often dominant. However, our assumptions of functional equivalence fail to consider the opportunity for divergence conferred by ~180 Million Years (MY) of independent evolution between these species. For a given set of human disease related genes, it is therefore important to determine if functional equivalency has been retained between species. In this study we test the hypothesis that cancer associated genes have different patterns of substitution akin to adaptive evolution in different mammal lineages. RESULTS: Our analysis of the current literature and colon cancer databases identified 22 genes exhibiting colon cancer associated germline mutations. We identified orthologs for these 22 genes across a set of high coverage (>6X) vertebrate genomes. Analysis of these orthologous datasets revealed significant levels of positive selection. Evidence of lineage-specific positive selection was identified in 14 genes in both ancestral and extant lineages. Lineage-specific positive selection was detected in the ancestral Euarchontoglires and Hominidae lineages for STK11, in the ancestral primate lineage for CDH1, in the ancestral Murinae lineage for both SDHC and MSH6 genes and the ancestral Muridae lineage for TSC1. CONCLUSION: Identifying positive selection in the primate, Hominidae, Muridae and Murinae lineages suggest an ancestral functional shift in these genes between the rodent and primate lineages. Analyses such as this, combining evolutionary theory and predictions - along with medically relevant data, can thus provide us with important clues for modeling human diseases.