Resolving ambiguity in the phylogenetic relationship of genotypes A, B, and C of hepatitis B virus.

Abstract:

BACKGROUND:Hepatitis B virus (HBV) is an important infectious agent that causes widespread concern because billions of people are infected by at least 8 different HBV genotypes worldwide. However, reconstruction of the phylogenetic relationship between HBV genotypes is difficult. Specifically, the phylogenetic relationships among genotypes A, B, and C are not clear from previous studies because of the confounding effects of genotype recombination. In order to clarify the evolutionary relationships, a rigorous approach is required that can effectively explore genetic sequences with recombination. RESULT:In the present study, phylogenetic relationship of the HBV genotypes was reconstructed using a consensus phylogeny of phylogenetic trees of HBV genome segments. Reliability of the reconstructed phylogeny was extensively evaluated in agreements of local phylogenies of genome segments.The reconstructed phylogenetic tree revealed that HBV genotypes B and C had a closer phylogenetic relationship than genotypes A and B or A and C. Evaluations showed the consensus method was capable to reconstruct reliable phylogenetic relationship in the presence of recombinants. CONCLUSION:The consensus method implemented in this study provides an alternative approach for reconstructing reliable phylogenetic relationships for viruses with possible genetic recombination. Our approach revealed the phylogenetic relationships of genotypes A, B, and C of HBV.

journal_name

BMC Evol Biol

journal_title

BMC evolutionary biology

authors

Jiang Y,Wang M,Zheng H,Wang WR,Jin L,He Y

doi

10.1186/1471-2148-13-120

subject

Has Abstract

pub_date

2013-06-11 00:00:00

pages

120

issn

1471-2148

pii

1471-2148-13-120

journal_volume

13

pub_type

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

    abstract: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. RES...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-1051-7

    authors: Xu S,Sun X,Niu X,Zhang Z,Tian R,Ren W,Zhou K,Yang G

    更新日期:2017-08-29 00:00:00

  • Dispersal strategies of phytophagous insects at a local scale: adaptive potential of aphids in an agricultural environment.

    abstract:BACKGROUND:The spread of agriculture greatly modified the selective pressures exerted by plants on phytophagous insects, by providing these insects with a high-level resource, structured in time and space. The life history, behavioural and physiological traits of some insect species may have evolved in response to thes...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-6-75

    authors: Lombaert E,Boll R,Lapchin L

    更新日期:2006-10-02 00:00:00

  • Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta.

    abstract:BACKGROUND:Metallothionein (mt) transcription is elevated in heavy metal tolerant field populations of Orchesella cincta (Collembola). This suggests that natural selection acts on transcriptional regulation of mt in springtails at sites where cadmium (Cd) levels in soil reach toxic values This study investigates the na...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-7-88

    authors: Janssens TK,Mariën J,Cenijn P,Legler J,van Straalen NM,Roelofs D

    更新日期:2007-06-11 00:00:00

  • Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts.

    abstract:BACKGROUND:Whole-genome duplication (WGD) events have shaped the genomes of eukaryotic organisms. Relaxed selection after duplication along with inherent functional constraints are thought to determine the fate of the paralogs and, ultimately, the evolution of gene function. Here, we investigated the rate of protein ev...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-0895-1

    authors: Ascencio D,Ochoa S,Delaye L,DeLuna A

    更新日期:2017-02-06 00:00:00

  • Molecular evolution of the vertebrate TLR1 gene family--a complex history of gene duplication, gene conversion, positive selection and co-evolution.

    abstract:BACKGROUND:The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Toll-like receptor superfamily have few paralogues; the exception is the TLR1 gene family with four clo...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-149

    authors: Huang Y,Temperley ND,Ren L,Smith J,Li N,Burt DW

    更新日期:2011-05-28 00:00:00

  • Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster.

    abstract:BACKGROUND:Drosophila melanogaster often shows correlations between latitude and phenotypic or genetic variation on different continents, which suggests local adaptation with respect to a heterogeneous environment. Previous phenotypic analyses of latitudinal clines have investigated mainly physiological, morphological,...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0316-2

    authors: Svetec N,Zhao L,Saelao P,Chiu JC,Begun DJ

    更新日期:2015-03-13 00:00:00

  • Lineage diversification and historical demography of a montane bird Garrulax elliotii--implications for the Pleistocene evolutionary history of the eastern Himalayas.

    abstract:BACKGROUND:Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in many extant species. In montane habitats, species' ranges may have expanded and contracted along an altitudinal gradient in response to environmental fluctuations leading to alternating periods of genetic isolation and...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-174

    authors: Qu Y,Luo X,Zhang R,Song G,Zou F,Lei F

    更新日期:2011-06-21 00:00:00

  • Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica.

    abstract:BACKGROUND:The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-019-1545-6

    authors: Pirie MD,Kandziora M,Nürk NM,Le Maitre NC,Mugrabi de Kuppler A,Gehrke B,Oliver EGH,Bellstedt DU

    更新日期:2019-12-05 00:00:00

  • Low reproductive skew despite high male-biased operational sex ratio in a glass frog with paternal care.

    abstract:BACKGROUND:Reproductive skew, the uneven distribution of reproductive success among individuals, is a common feature of many animal populations. Several scenarios have been proposed to favour either high or low levels of reproductive skew. Particularly a male-biased operational sex ratio and the asynchronous arrival of...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0469-z

    authors: Mangold A,Trenkwalder K,Ringler M,Hödl W,Ringler E

    更新日期:2015-09-03 00:00:00

  • Ecological niche and phylogeography elucidate complex biogeographic patterns in Loxosceles rufescens (Araneae, Sicariidae) in the Mediterranean Basin.

    abstract:BACKGROUND:Understanding the evolutionary history of morphologically cryptic species complexes is difficult, and made even more challenging when geographic distributions have been modified by human-mediated dispersal. This situation is common in the Mediterranean Basin where, aside from the environmental heterogeneity ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-014-0195-y

    authors: Planas E,Saupe EE,Lima-Ribeiro MS,Peterson AT,Ribera C

    更新日期:2014-10-09 00:00:00

  • A genome-wide scan for genes under balancing selection in Drosophila melanogaster.

    abstract:BACKGROUND:In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plant...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-016-0857-z

    authors: Croze M,Wollstein A,Božičević V,Živković D,Stephan W,Hutter S

    更新日期:2017-01-13 00:00:00

  • Histone modification pattern evolution after yeast gene duplication.

    abstract:BACKGROUND:Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression diverg...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-12-111

    authors: Zou Y,Su Z,Huang W,Gu X

    更新日期:2012-07-09 00:00:00

  • Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae).

    abstract:BACKGROUND:The spatial distribution of genetic diversity and structure has important implications for conservation as it reveals a species' strong and weak points with regard to stability and evolutionary capacity. Temporal genetic stability is rarely tested in marine species other than commercially important fishes, b...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-018-1213-2

    authors: Jueterbock A,Coyer JA,Olsen JL,Hoarau G

    更新日期:2018-06-15 00:00:00

  • Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos.

    abstract:BACKGROUND:Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-0905-3

    authors: Gillingham MA,Béchet A,Courtiol A,Rendón-Martos M,Amat JA,Samraoui B,Onmuş O,Sommer S,Cézilly F

    更新日期:2017-02-20 00:00:00

  • Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis.

    abstract:BACKGROUND:Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactio...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章,meta分析

    doi:10.1186/s12862-016-0698-9

    authors: Rúa MA,Antoninka A,Antunes PM,Chaudhary VB,Gehring C,Lamit LJ,Piculell BJ,Bever JD,Zabinski C,Meadow JF,Lajeunesse MJ,Milligan BG,Karst J,Hoeksema JD

    更新日期:2016-06-10 00:00:00

  • Strength and tempo of selection revealed in viral gene genealogies.

    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 ...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-220

    authors: Bedford T,Cobey S,Pascual M

    更新日期:2011-07-25 00:00:00

  • The effect of three environmental conditions on the fitness of cytochrome P450 monooxygenase-mediated permethrin resistance in Culex pipiens quinquefasciatus.

    abstract:BACKGROUND:The evolution of insecticide resistance and persistence of resistance phenotypes are influenced by the fitness of resistance alleles in the absence of insecticide pressure. Experimental determination of fitness is difficult, but fitness can be inferred by measuring changes in allele frequencies in appropriat...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-9-42

    authors: Hardstone MC,Lazzaro BP,Scott JG

    更新日期:2009-02-19 00:00:00

  • Worthless donations: male deception and female counter play in a nuptial gift-giving spider.

    abstract:BACKGROUND:In nuptial gift-giving species, benefits of acquiring a mate may select for male deception by donation of worthless gifts. We investigated the effect of worthless gifts on mating success in the spider Pisaura mirabilis. Males usually offer an insect prey wrapped in silk; however, worthless gifts containing i...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-329

    authors: Albo MJ,Winther G,Tuni C,Toft S,Bilde T

    更新日期:2011-11-14 00:00:00

  • Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges.

    abstract:BACKGROUND:One of the hallmarks of multicellular organisms is the ability of their cells to trigger responses to the environment in a coordinated manner. In recent years primary cilia have been shown to be present as 'antennae' on almost all animal cells, and are involved in cell-to-cell signaling in development and ti...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-14-3

    authors: Ludeman DA,Farrar N,Riesgo A,Paps J,Leys SP

    更新日期:2014-01-13 00:00:00

  • Molecular evolution of a chordate specific family of G protein-coupled receptors.

    abstract:BACKGROUND:Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-11-234

    authors: Kurtenbach S,Mayer C,Pelz T,Hatt H,Leese F,Neuhaus EM

    更新日期:2011-08-09 00:00:00

  • Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes.

    abstract:BACKGROUND:Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta. In the human and mouse genomes, Tex19 and Secre...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0506-y

    authors: Bianchetti L,Tarabay Y,Lecompte O,Stote R,Poch O,Dejaegere A,Viville S

    更新日期:2015-10-12 00:00:00

  • D- and L-lactate dehydrogenases during invertebrate evolution.

    abstract:BACKGROUND:The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of pyruvate to L(-)-lactate and D(+)-lactate, belong to evolutionarily unrelated enzyme families. The genes encoding L-LDH have been used as a model for gene duplication due to the multiple paralogs found in eubacteria, archaebac...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-8-268

    authors: Cristescu ME,Innes DJ,Stillman JH,Crease TJ

    更新日期:2008-10-01 00:00:00

  • RUNX2 repeat variation does not drive craniofacial diversity in marsupials.

    abstract:BACKGROUND:Runt-related transcription factor 2 (RUNX2) is a transcription factor essential for skeletal development. Variation within the RUNX2 polyglutamine / polyalanine (QA) repeat is correlated with facial length within orders of placental mammals and is suggested to be a major driver of craniofacial diversity. How...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-0955-6

    authors: Newton AH,Feigin CY,Pask AJ

    更新日期:2017-05-04 00:00:00

  • Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean.

    abstract:BACKGROUND:The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphol...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-14-92

    authors: Nguyen VX,Detcharoen M,Tuntiprapas P,Soe-Htun U,Sidik JB,Harah MZ,Prathep A,Papenbrock J

    更新日期:2014-04-30 00:00:00

  • Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants.

    abstract:BACKGROUND:The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-bonds in alpha, beta-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multig...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-9-90

    authors: Li W,Liu B,Yu L,Feng D,Wang H,Wang J

    更新日期:2009-05-05 00:00:00

  • Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae.

    abstract:BACKGROUND:The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never r...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-0935-x

    authors: Flores-Ponce M,Vallebueno-Estrada M,González-Orozco E,Ramos-Aboites HE,García-Chávez JN,Simões N,Montiel R

    更新日期:2017-04-26 00:00:00

  • The effect of body size evolution and ecology on encephalization in cave bears and extant relatives.

    abstract:BACKGROUND:The evolution of larger brain volumes relative to body size in Mammalia is the subject of an extensive amount of research. Early on palaeontologists were interested in the brain of cave bears, Ursus spelaeus, and described its morphology and size. However, until now, it was not possible to compare the absolu...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-017-0976-1

    authors: Veitschegger K

    更新日期:2017-06-05 00:00:00

  • Cheating does not explain selective differences at high and low relatedness in a social amoeba.

    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

    authors: Saxer G,Brock DA,Queller DC,Strassmann JE

    更新日期:2010-03-12 00:00:00

  • Tooth and scale morphogenesis in shark: an alternative process to the mammalian enamel knot system.

    abstract:BACKGROUND:The gene regulatory network involved in tooth morphogenesis has been extremely well described in mammals and its modeling has allowed predictions of variations in regulatory pathway that may have led to evolution of tooth shapes. However, very little is known outside of mammals to understand how this regulat...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/s12862-015-0557-0

    authors: Debiais-Thibaud M,Chiori R,Enault S,Oulion S,Germon I,Martinand-Mari C,Casane D,Borday-Birraux V

    更新日期:2015-12-24 00:00:00

  • Are substitution rates and RNA editing correlated?

    abstract:BACKGROUND:RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are f...

    journal_title:BMC evolutionary biology

    pub_type: 杂志文章

    doi:10.1186/1471-2148-10-349

    authors: Cuenca A,Petersen G,Seberg O,Davis JI,Stevenson DW

    更新日期:2010-11-11 00:00:00