Abstract：
BACKGROUND:RNA viruses evolve extremely quickly, allowing them to rapidly adapt to new environmental conditions. Viral pathogens, such as influenza virus, exploit this capacity for evolutionary change to persist within the human population despite substantial immune pressure. Understanding the process of adaptation in these viral systems is essential to our efforts to combat infectious disease. RESULTS:Through analysis of simulated populations and sequence data from influenza A (H3N2) and measles virus, we show how phylogenetic and population genetic techniques can be used to assess the strength and temporal pattern of adaptive evolution. The action of natural selection affects the shape of the genealogical tree connecting members of an evolving population, causing deviations from the neutral expectation. The magnitude and distribution of these deviations lends insight into the historical pattern of evolution and adaptation in the viral population. We quantify the degree of ongoing adaptation in influenza and measles virus through comparison of census population size and effective population size inferred from genealogical patterns, finding a 60-fold greater deviation in influenza than in measles. We also examine the tempo of adaptation in influenza, finding evidence for both continuous and episodic change. CONCLUSIONS:Our results have important consequences for understanding the epidemiological and evolutionary dynamics of the influenza virus. Additionally, these general techniques may prove useful to assess the strength and pattern of adaptive evolution in a variety of evolving systems. They are especially powerful when assessing selection in fast-evolving populations, where temporal patterns become highly visible.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Bedford T,Cobey S,Pascual Mdoi
10.1186/1471-2148-11-220subject
Has Abstractpub_date
2011-07-25 00:00:00pages
220issn
1471-2148pii
1471-2148-11-220journal_volume
11pub_type
杂志文章abstract：BACKGROUND:Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-12-6
更新日期：2012-01-17 00:00:00
abstract：BACKGROUND:The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-13-258
更新日期：2013-11-21 00:00:00
abstract：BACKGROUND:Speciation often occurs in complex or uncertain temporal and spatial contexts. Processes such as reinforcement, allopatric divergence, and assortative mating can proceed at different rates and with different strengths as populations diverge. The Central American Midas cichlid fish species complex is an impor...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-7-25
更新日期：2007-02-20 00:00:00
abstract：BACKGROUND:Early evolutionary theories of aging predict that populations which experience low extrinsic mortality evolve a retarded onset of senescence. Experimental support for this theory in vertebrates is scarce, in part for the difficulty of quantifying extrinsic mortality and its condition- and density-dependent c...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-13-77
更新日期：2013-04-03 00:00:00
abstract：BACKGROUND:Tanabin, transitin and nestin are type VI intermediate filament (IF) proteins that are developmentally regulated in frogs, birds and mammals, respectively. Tanabin is expressed in the growth cones of embryonic vertebrate neurons, whereas transitin and nestin are found in myogenic and neurogenic cells. Anothe...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-7-164
更新日期：2007-09-13 00:00:00
abstract：BACKGROUND:Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adult...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-014-0170-7
更新日期：2014-08-28 00:00:00
abstract：BACKGROUND:Homeobox genes are the key regulators during development, and they are in general highly conserved with only a few reported cases of rapid evolution. RHOXF2 is an X-linked homeobox gene in primates. It is highly expressed in the testicle and may play an important role in spermatogenesis. As male reproductive...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-11-298
更新日期：2011-10-12 00:00:00
abstract：BACKGROUND:Genetic analyses of DNA sequences make use of an increasingly complex set of nucleotide substitution models to estimate the divergence between gene sequences. However, there is currently no way to assess the validity of nucleotide substitution models over short time-scales and with limited mutational accumul...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0312-6
更新日期：2015-03-11 00:00:00
abstract：BACKGROUND:Genetic breaks separating regional lineages of marine organisms with potentially high broadcasting abilities are generally attributed either to dispersal barriers such as currents or upwelling, or to behavioural strategies promoting self-recruitment. We investigated whether such patterns could potentially al...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-341
更新日期：2008-12-24 00:00:00
abstract：BACKGROUND:While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-4-31
更新日期：2004-09-09 00:00:00
abstract：BACKGROUND:Altruism can be favored by high relatedness among interactants. We tested the effect of relatedness in experimental populations of the social amoeba Dictyostelium discoideum, where altruism occurs in a starvation-induced social stage when some amoebae die to form a stalk that lifts the fertile spores above t...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-10-76
更新日期：2010-03-12 00:00:00
abstract：BACKGROUND:Phylactolaemata is commonly regarded the earliest branch within Bryozoa and thus the sister group to the other bryozoan taxa, Cyclostomata and Gymnolaemata. Therefore, the taxon is important for the reconstruction of the bryozoan morphological ground pattern. In this study the myoanatomy of Pectinatella magn...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-017-1068-y
更新日期：2017-11-07 00:00:00
abstract：BACKGROUND:Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-10-144
更新日期：2010-05-17 00:00:00
abstract：BACKGROUND:Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-11-20
更新日期：2011-01-20 00:00:00
abstract：BACKGROUND:Many groups of land snails show great interspecific diversity in shell ornamentation, which may include spines on the shell and flanges on the aperture. Such structures have been explained as camouflage or defence, but the possibility that they might be under sexual selection has not previously been explored...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-3-13
更新日期：2003-06-05 00:00:00
abstract：BACKGROUND:The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0400-7
更新日期：2015-06-30 00:00:00
abstract：BACKGROUND:Remipedia, a group of homonomously segmented, cave-dwelling, eyeless arthropods have been regarded as basal crustaceans in most early morphological and taxonomic studies. However, molecular sequence information together with the discovery of a highly differentiated brain led to a reconsideration of their phy...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-12-168
更新日期：2012-09-05 00:00:00
abstract：BACKGROUND:The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-6-89
更新日期：2006-11-07 00:00:00
abstract：BACKGROUND:In plants the hormone cytokinin is perceived by members of a small cytokinin receptor family, which are hybrid sensor histidine kinases. While the immediate downstream signaling pathway is well characterized, the domain of the receptor responsible for ligand binding and which residues are involved in this pr...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-7-62
更新日期：2007-04-17 00:00:00
abstract：BACKGROUND:Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-014-0264-2
更新日期：2014-12-21 00:00:00
abstract：BACKGROUND:There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by al...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-019-1464-6
更新日期：2019-07-30 00:00:00
abstract：BACKGROUND:ADP-glucose pyrophosphorylase (AGPase), which catalyses a rate limiting step in starch synthesis, is a heterotetramer comprised of two identical large and two identical small subunits in plants. Although the large and small subunits are equally sensitive to activity-altering amino acid changes when expressed...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-8-232
更新日期：2008-08-12 00:00:00
abstract：BACKGROUND:Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroev...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-12-88
更新日期：2012-06-14 00:00:00
abstract：BACKGROUND:While numerous studies revealed the major role of environmental changes of the Quaternary on the evolution of biodiversity, research on the influence of that period on current South-American fauna is scarce and have usually focused on lowland regions. In this study, the genetic structure of the pampas cat (L...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-9-68
更新日期：2009-03-30 00:00:00
abstract：BACKGROUND:The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversi...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-017-1066-0
更新日期：2017-10-26 00:00:00
abstract：BACKGROUND:During past glacial periods, many species of forest-dwelling animals experienced range contractions. In contrast, species living outside such moist habitats appear to have reacted to Quaternary changes in different ways. The Atlantic Forest represents an excellent opportunity to test phylogeographic hypothes...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0383-4
更新日期：2015-06-10 00:00:00
abstract：BACKGROUND:The seacoasts of the Japanese Arc are fringed by many gravel beaches owing to active tectonic uplift and intense denudation caused by heavy rainfall. These gravel beaches are inhabited by gobies of the genus Luciogobius that burrow into the gravel sediment and live interstitially. Although their habitat and ...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/1471-2148-9-145
更新日期：2009-06-28 00:00:00
abstract：BACKGROUND:The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates a...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0456-4
更新日期：2015-08-26 00:00:00
abstract：BACKGROUND:Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. RES...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-019-1472-6
更新日期：2019-07-23 00:00:00
abstract：BACKGROUND:Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both fie...
journal_title：BMC evolutionary biology
pub_type： 杂志文章
doi：10.1186/s12862-015-0297-1
更新日期：2015-02-10 00:00:00
