Evidence For Adaptive Evolution Research Articles

VIPERA: Viral Intra-Patient Evolution Reporting and Analysis.

Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.

Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages.

The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, Entamoeba and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.

Positive selection in the mitochondrial protein coding genes of teleost regional endotherms: Evidence for adaptive evolution

Marine biology,marine ecology,Phytoplankton, marine algae, zooplankton, nekton, benthos, corals and coral reefs, ecology, zoogeography and systematics, primary production and experimental work on ecosystem including energy flow at different trophic levels, population dynamics and theoretical models, recycling of matter, influence of environmental factors on metabolic activity, marine microbiology, mariculture and experimental work on propagation of cultivable species, biology of fishes, marine reptiles, sea birds and mammals, physical, chemical, geological and meteorological features of the environments related to marine biology, marine environmental damage caused by pollution and engineering works, underwater observations, conservation of living resources, modifications in methodology and techniques and development of new apparatus related to marine sciences

A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles.

The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this study, we present the most comprehensive phylogenetic and phylogeographic analysis, contributing to a better understanding of the origins, diversification, and the role of different host species in the evolution and diffusion of a dog-related variant endemic of South America. A total of 237 complete Nucleoprotein gene sequences were studied, corresponding to wild and domestic species, performing selection analyses, ancestral states reconstructions, and recombination analyses. This variant originated in Brazil and disseminated through Argentina and Paraguay, where a previously unknown lineage was found. A single host shift was identified in the phylogeny, from dog to the crab-eating fox (Cerdocyon thous) in the Northeast of Brazil. Although this process occurred in a background of purifying selection, there is evidence of adaptive evolution -or selection of sub-consensus sequences- in internal branches after the host shift. The interaction of domestic and wild cycles persisted after host switching, as revealed by spillover and putative recombination events.

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

BackgroundIn genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution.ResultsPhylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch.ConclusionsThe mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.

Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates

Early in life, infants are colonized with multiple bacterial strains whose differences in gene content can have important health consequences. Metagenomics-based approaches have revealed gene content differences between different strains co-colonizing newborns, but less is known about the rate, mechanism, and phenotypic consequences of gene content diversification within strains. Here, focusing on Staphylococcus epidermidis, we whole-genome sequence and phenotype more than 600 isolates from newborns. Within days of birth, infants are co-colonized with a highly personalized repertoire of S. epidermidis strains, which are spread across the newborn body. Comparing the genomes of multiple isolates of each strain, we find very little evidence of adaptive evolution via single-nucleotide polymorphisms. By contrast, we observe gene content differences even between otherwise genetically identical cells, including variation of the clinically important methicillin resistance gene, mecA, suggesting rapid gene gain and loss events at rates higher than point mutations. Mapping the genomic architecture of structural variants by long-read Nanopore sequencing, we find that deleted regions were always flanked by direct repeats, consistent with site-specific recombination. However, we find that even within a single genetic background, recombination occurs at multiple, often non-canonical repeats, leading to the rapid evolution of patient-specific diverse structural variants in the SCCmec island and to differences in antibiotic resistance.

Evidence of Adaptive Evolution in Wolbachia-Regulated Gene DNMT2 and Its Role in the Dipteran Immune Response and Pathogen Blocking.

Eukaryotic nucleic acid methyltransferase (MTase) proteins are essential mediators of epigenetic and epitranscriptomic regulation. DNMT2 belongs to a large, conserved family of DNA MTases found in many organisms, including holometabolous insects such as fruit flies and mosquitoes, where it is the lone MTase. Interestingly, despite its nomenclature, DNMT2 is not a DNA MTase, but instead targets and methylates RNA species. A growing body of literature suggests that DNMT2 mediates the host immune response against a wide range of pathogens, including RNA viruses. Curiously, although DNMT2 is antiviral in Drosophila, its expression promotes virus replication in mosquito species. We, therefore, sought to understand the divergent regulation, function, and evolution of these orthologs. We describe the role of the Drosophila-specific host protein IPOD in regulating the expression and function of fruit fly DNMT2. Heterologous expression of these orthologs suggests that DNMT2′s role as an antiviral is host-dependent, indicating a requirement for additional host-specific factors. Finally, we identify and describe potential evidence of positive selection at different times throughout DNMT2 evolution within dipteran insects. We identify specific codons within each ortholog that are under positive selection and find that they are restricted to four distinct protein domains, which likely influence substrate binding, target recognition, and adaptation of unique intermolecular interactions. Collectively, our findings highlight the evolution of DNMT2 in Dipteran insects and point to structural, regulatory, and functional differences between mosquito and fruit fly homologs.

Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, VSBV-1).

Mammalian 2 orthobornavirus (VSBV-1) is an emerging zoonotic pathogen discovered in several exotic squirrel species and associated with fatal human encephalitis. The dynamics of VSBV-1 spread and evolution in its presumed natural hosts are unknown. Here, we present the phylogeny, micro-evolution, cross-species transmission and spread of VSBV-1 at a temporal and spatial resolution within the limits of animal husbandry. The results showed that VSBV-1 can be classified into six distinct groups and that the most recent common ancestor of the known German strains emerged at least 20 years ago. We here demonstrate that the genetic diversity of the VSBV-1 groups is shaped primarily by in situ evolution and most of the amino acid changes are deleterious polymorphisms removed by purifying selection. Evidence of adaptive evolution has been found in the G and L genes which might have an influence on transmission fitness. Furthermore, there was also evidence for some form of adaptive changes in the glycoprotein which suggests that many sites might be subjected to positive pressure evolving under episodic directional selection, indicating past occurrence of positive selection. Host switching events were detected as dominant evolutionary mechanisms driving the virus-host associations. Virus spread by animal trade followed by subsequent local micro-evolution in zoos and holdings is responsible for diversifying strains. Time-resolved phylogeny indicated that Prevost’s squirrels might be the original squirrel species carrying and seeding the virus in Germany. This study provides the first insight into the ecology and micro-evolutionary dynamics of this novel viral pathogen in the captive exotic squirrel population under artificial ecological conditions (zoos and animal husbandry) and co-housing of different squirrel species.

Rapid evolution of latitudinal clines in growth and defence of an invasive weed.

Re-establishment of heritable latitudinal clines in growth-related traits has been recognised as evidence for adaptive evolution in invasive plants. However, less information is known about latitudinal clines in defence and joint clinal evolution of growth and defence in invasive plants. We planted 14 native Argentinean populations and 14 introduced Chinese populations of Alternanthera philoxeroides in replicate common gardens in China. We investigated the latitudinal clines of traits related to growth and defence, and plasticity of these traits in relation to experiment site and soil nitrogen. We found that chemical defence decreased with latitude in introduced populations but increased with latitude in native populations. For growth rate, latitudinal clines were positive in introduced populations but nonexistent in native populations. There were also parallel positive latitudinal clines in total/shoot biomass and specific leaf area. Experiment site affected the occurrence or magnitude of latitudinal clines in growth rate, branch intensity and triterpenoid saponins concentration. Introduced populations were more plastic to experiment site and soil nitrogen than native populations. We provide evidence for rapid evolution of clines in growth and defence in an invasive plant. Altered herbivory gradients and trade-off between growth and defence may explain nonparallel clines between the native and introduced ranges.

Molecular Evolution of Antigen-Processing Genes in Salamanders: Do They Coevolve with MHC Class I Genes?

Proteins encoded by antigen-processing genes (APGs) prepare antigens for presentation by the major histocompatibility complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MHC I. In addition, APGs should evolve under positive selection, a consequence of the adaptive evolution in MHC I. The presence of multiple highly expressed MHC I genes in some teleosts, birds, and urodeles appears incompatible with the coevolution hypothesis. Here, we use urodele amphibians to test two key expectations derived from the coevolution hypothesis: 1) the linkage between APGs and MHC I was studied in Lissotriton newts and 2) the evidence for adaptive evolution in APGs was assessed using 42 urodele species comprising 21 genera from seven families. We demonstrated that five APGs (PSMB8, PSMB9, TAP1, TAP2, and TAPBP) are tightly linked (<0.5 cM) to MHC I. Although all APGs showed some codons under episodic positive selection, we did not find a pervasive signal of positive selection expected under the coevolution hypothesis. Gene duplications, putative gene losses, and divergent allelic lineages detected in some APGs demonstrate considerable evolutionary dynamics of APGs in salamanders. Overall, our results indicate that if coevolution between APGs and MHC I occurred in urodeles, it would be more complex than envisaged in the original formulation of the hypothesis.

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e.

Seasonal coronaviruses (OC43, 229E, NL63, and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here we address the influence of antigenic drift on immune evasion of seasonal coronaviruses. We provide evidence that at least two of these viruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively selected genetic changes in these viruses that enable them to escape recognition by the immune system. It is possible that, as with seasonal influenza, these adaptive changes in antigenic regions of the virus would necessitate continual reformulation of a vaccine made against them.

Convergent evolution of tail spines in squamate reptiles driven by microhabitat use

The repeated evolution of convergent or analogous traits is often used as evidence for adaptive evolution. Squamate reptiles show a high degree of convergence in a variety of morphological traits; however, the evolutionary mechanisms driving these patterns are not fully understood. Here, we investigate the evolution of tail spines, a trait that evolved multiple times in evolutionarily independent clades of lizards. Taking a comparative phylogenetic approach, we use 2877 squamate species to demonstrate that the evolution of spiny tails is correlated with microhabitat use, with species that live in rocky habitats significantly more likely to have evolved spiny tails. In the light of previous behavioural observations, our results suggest that spiny-tailed lizards have an advantage in rocky habitats through predation avoidance, where tail spines are used to prevent extraction from rocky crevices. In concordance with previous research on lizard body armour, our results suggest that the evolution of tail spines is coupled to both a rock-dwelling lifestyle and predator avoidance strategies, and highlight a complex interplay between different selective pressures on the evolution of defensive morphologies in reptiles.

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation.

Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota remains elusive. We used Hi-C (High-throughput chromosomal conformation capture), coupled with probabilistic modeling of experimental noise, to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two subjects, including 12,251 accessory elements. Comparisons of 2 samples collected 10 years apart for each of the subjects revealed extensive in situ exchange of accessory elements, as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult subjects. This work provides a foundation and approach for studying microbial evolution in natural environments.

An experimentally introduced population of Brassica rapa (Brassicaceae). 2. Rapid evolution of phenotypic traits

Background and aims – Introduced populations can potentially experience strong selection and rapid evolution. While some retrospective studies have shown rapid evolution in introduced populations in the past, few have directly tested for and characterized evolution as it occurs. Here we use an experimental introduction to directly observe and quantify evolution of multiple traits in a plant population introduced to a novel environment. Methods – We experimentally introduced seeds of the annual plant Brassica rapa L. (Brassicaceae) from a location in southern California into multiple replicated plots in New York. We allowed the populations to naturally evolve for 3 years. Following the resurrection approach, we compared ancestors and descendants planted in common garden conditions in New York in multiple phenotypic traits. Key results – Within only three generations, there was significant evolution of several morphological, phenological, and fitness traits, as well as substantial variation among traits. Despite selection for larger size during the three years following introduction, there was evolution of smaller size, earlier flowering time, and shorter duration of flowering. Although there were rapid evolutionary changes in traits, descendants did not have greater fitness than ancestors in New York, indicating a lack of evidence for adaptive evolution, at least over the timeframe of the study. Conclusions – This study found rapid evolution of several morphological and phenological traits, including smaller plant size and shorter time to flowering, following introduction, confirming that evolution can rapidly occur during the early stages of colonization. Many traits evolved in the opposite direction predicted from phenotypic selection analysis, which suggests that the resurrection approach can reveal unanticipated evolutionary changes and can be very useful for studying contemporary evolution.

Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)

BackgroundLeaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood.ResultsEight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period.ConclusionsChanges of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.

Genomic footprint of evolution of eusociality in bees: floral food use and CYPome “blooms”

Comparative analyses of genomes of ten bee species representing different degrees of social complexity have demonstrated that independent transitions to eusociality are often accompanied by or lead to expansions or contractions of gene families (albeit different families across independent lineages). Because collective gathering, processing, and storage of plant products is a hallmark of bee social complexity, we examined the genomic inventory of cytochrome P450 genes (the CYPome) in these ten genomes, to search for footprints of eusociality in phytochemical detoxification pathways and, using a Bayesian implementation of the McDonald–Kreitman test, evidence of adaptive evolution within P450 lineages associated with food processing in eusocial florivorous Bombus and Apis species versus eusocial carnivorous Polistes species.We found no patterns linking CYPome size to level of social complexity within the ten bee genomes at the gene family level; however, a pattern emerged at the subfamily level, with the CYP6AS subfamily most diverse in perennial eusocial resin-collecting bees. In Apis mellifera, several CYP6AS enzymes are known to metabolize flavonols, ubiquitous constituents of nectar and honey, pollen and beebread, and resins and propolis. CYP6AS subfamily size varies from 7 in the solitary Habropoda laboriosa and the facultatively eusocial Lasioglossum albipes to 17 in the perennial eusocial Melipona quadrifasciatus; the degree of sociality across the ten species is correlated with CYP6AS inventory size (Spearman’s rho = 0.704, p < 0.023). Remarkably, there is perfect overlap between CYP6AS genes upregulated by the flavonol quercetin in A. mellifera and CYP6AS genes with signs of adaptive evolution in either Apis or Bombus. Our finding of positive selection on CYP6AS genes in Apis and Bombus, but not Polistes supports the hypothesis that CYP6AS subfamily expansion was involved in facilitating the shift from carnivory to florivory in bees. That some CYP6AS enzymes metabolize flavonoids suggests that subfamily expansion results from increased evolutionary exposure to these phytochemicals, through concentration of nectar into honey, pollen into beebread, and plant resins into propolis. Accompanying the evolutionary progression from solitary to perennial eusocial behavior in bees is a transition from short-term storage of ephemeral low-quality resources to concentrating and stockpiling those resources for colony use, with a concomitant need for phytochemical detoxification.

Evidence of Adaptive Evolution and Relaxed Constraints in Sex-Biased Genes of South American and West Indies Fruit Flies (Diptera: Tephritidae).

Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and nonadaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and Anastrepha obliqua, a pair of species that have diverged recently, likely in the presence of gene flow. Using these data, we inferred differentiation indexes and evolutionary rates and tested for signals of selection in thousands of genes expressed in head and reproductive transcriptomes from both species. Our results indicate that sex-biased and reproductive-biased genes evolve faster than unbiased genes in both species, which is due to both adaptive pressure and relaxed constraints. Furthermore, among male-biased genes evolving under positive selection, we identified some related to sexual functions such as courtship behavior and fertility. These findings suggest that sex-biased genes may have played important roles in the establishment of reproductive isolation between these species, due to a combination of selection and drift, and unveil a plethora of genetic markers useful for more studies in these species and their differentiation.

The transcriptome response of Heliconius melpomene larvae to a novel host plant.

In the warfare between herbivore and host plant, insects have evolved a variety of defensive mechanisms, including allelochemical transformation and excretion. Several studies have explored the transcriptome responses of insects after host plant shifts to understand these mechanisms. We investigated the plastic responses of Heliconius melpomene larvae feeding on a native host Passiflora menispermifolia and a less strongly defended nonhost species, Passiflora biflora. In total, 326 differentially expressed genes were identified, with a greater number upregulated on the more strongly defended native host. Functional annotation showed that detoxifying enzymes, transporters and components of peritrophic membrane were strongly represented. In total, 30 candidate detoxification genes were differentially expressed, with glutathione S-transferases (GSTs) and UDP-glucuronosyltransferases (UGTs) showing the highest proportion of differential expression, 27.3% and 17.3%, respectively. These differentially expressed detoxification genes were shown to evolve mainly under the influence of purifying selection, suggesting that protein-coding evolution has not played a major role in host adaptation. We found only one gene, GSTe3, with evidence of adaptive evolution at H40, which is around the G-site and might alter enzyme activity. Based on our transcriptome and molecular evolution analysis, we suggest that transcriptional plasticity of genes in a herbivore may play an important role in adaptation to a new host plant.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers. How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.

Evidence of adaptive evolution of alpine pheasants to high-altitude environment from mitogenomic perspective

Adaptive evolutions to high-altitude adaptation have been intensively studied in mammals. However, considering the additional vertebrate groups, new perception regarding selection challenged by high-altitude stress on mitochondrial genome can be gained. To test this hypothesis, we compiled and analyzed the mitochondrial genomes of 5 alpine pheasants and 12 low-altitude species in Phasianidae. The results that evolutionary rates of ATP6 and ND6 showing significant fluctuation among branches when involved with five alpine pheasants revealed both genes might have implications with adapting to highland environment. The radical physico-chemical property changes identified by the modified MM01 model, including composition (C) and equilibrium constant (ionization of COOH) (Pk′) in ATP6 and beta-structure tendencies (Pβ), Pk′, and long-range non-bonded energy (El) in ND6, suggested that minor overall adjustments in size, protein conformation and relative orientation of reaction interfaces have been optimized to provide the ideal environments for electron transfer, proton translocation and generation of adenosine triphosphate (ATP). Additionally, three unique substitution sites were identified under selection in ND6, which could be potentially important adaptive changes contributing to cellular energy production. Our findings suggested that adaptive evolution may occur in alpine pheasants, which are an important complement to the knowledge of genetic mechanisms against the high-altitude environment in non-mammal animals.