Abstract:
BACKGROUND:The entire evolutionary history of life can be studied using myriad sequences generated by genomic research. This includes the appearance of the first cells and of superkingdoms Archaea, Bacteria, and Eukarya. However, the use of molecular sequence information for deep phylogenetic analyses is limited by mutational saturation, differential evolutionary rates, lack of sequence site independence, and other biological and technical constraints. In contrast, protein structures are evolutionary modules that are highly conserved and diverse enough to enable deep historical exploration. RESULTS:Here we build phylogenies that describe the evolution of proteins and proteomes. These phylogenetic trees are derived from a genomic census of protein domains defined at the fold family (FF) level of structural classification. Phylogenomic trees of FF structures were reconstructed from genomic abundance levels of 2,397 FFs in 420 proteomes of free-living organisms. These trees defined timelines of domain appearance, with time spanning from the origin of proteins to the present. Timelines are divided into five different evolutionary phases according to patterns of sharing of FFs among superkingdoms: (1) a primordial protein world, (2) reductive evolution and the rise of Archaea, (3) the rise of Bacteria from the common ancestor of Bacteria and Eukarya and early development of the three superkingdoms, (4) the rise of Eukarya and widespread organismal diversification, and (5) eukaryal diversification. The relative ancestry of the FFs shows that reductive evolution by domain loss is dominant in the first three phases and is responsible for both the diversification of life from a universal cellular ancestor and the appearance of superkingdoms. On the other hand, domain gains are predominant in the last two phases and are responsible for organismal diversification, especially in Bacteria and Eukarya. CONCLUSIONS:The evolution of functions that are associated with corresponding FFs along the timeline reveals that primordial metabolic domains evolved earlier than informational domains involved in translation and transcription, supporting the metabolism-first hypothesis rather than the RNA world scenario. In addition, phylogenomic trees of proteomes reconstructed from FFs appearing in each of the five phases of the protein world show that trees reconstructed from ancient domain structures were consistently rooted in archaeal lineages, supporting the proposal that the archaeal ancestor is more ancient than the ancestors of other superkingdoms.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Kim KM,Caetano-Anollés Gdoi
10.1186/1471-2148-12-13subject
Has Abstractpub_date
2012-01-27 00:00:00pages
13issn
1471-2148pii
1471-2148-12-13journal_volume
12pub_type
杂志文章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
更新日期:2018-06-15 00:00:00
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
更新日期:2011-08-09 00:00:00
abstract:BACKGROUND:Maternally inherited endosymbionts like Wolbachia pipientis are in linkage disequilibrium with the mtDNA of their hosts. Therefore, they can induce selective sweeps, decreasing genetic diversity over many generations. This sex ratio distorter, that is involved in the origin of parthenogenesis and other repro...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-340
更新日期:2010-11-04 00:00:00
abstract:BACKGROUND:The var genes of the human malaria parasite Plasmodium falciparum are highly polymorphic loci coding for the erythrocyte membrane proteins 1 (PfEMP1), which are responsible for the cytoaherence of P. falciparum infected red blood cells to the human vasculature. Cytoadhesion, coupled with differential express...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-110
更新日期:2013-05-31 00:00:00
abstract:BACKGROUND:Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4+ across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in euka...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0850-6
更新日期:2017-01-03 00:00:00
abstract:BACKGROUND:Prior to the sequencing of the human genome it was typically assumed that, tandem duplication aside, gene order is for the most part random. Numerous observers, however, highlighted instances in which a ligand was linked to one of its cognate receptors, with some authors suggesting that this may be a general...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-5-62
更新日期:2005-11-08 00:00:00
abstract:BACKGROUND:How vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (vertebrates, annelids, a few arthropod and mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigen...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01714-4
更新日期:2020-12-29 00:00:00
abstract:BACKGROUND:Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0362-9
更新日期:2015-06-11 00:00:00
abstract:BACKGROUND:Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-196
更新日期:2012-10-02 00:00:00
abstract:BACKGROUND:Sperm storage plays a key role in the reproductive success of many sexually-reproducing organisms, and the capacity of long-term sperm storage varies across species. While there are theoretical explanations for why such variation exists, to date there are no controlled empirical tests of the reproductive con...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01704-6
更新日期:2020-11-30 00:00:00
abstract:BACKGROUND:The evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly d...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-183
更新日期:2013-09-04 00:00:00
abstract:BACKGROUND:Chaetognaths, or arrow worms, are small marine, bilaterally symmetrical metazoans. The objective of this study was to analyse ribosomal protein (RP) coding sequences from a published collection of expressed sequence tags (ESTs) from a chaetognath (Spadella cephaloptera) and to use them in phylogenetic studie...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-146
更新日期:2007-08-28 00:00:00
abstract:BACKGROUND:Polymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalman...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-227
更新日期:2010-07-27 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:A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this report we have addressed the impact of factors like the universal distribution of the genes, their es...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-7-S1-S7
更新日期:2007-02-08 00:00:00
abstract::Recently, a set of publications described flea fossils from Jurassic and Early Cretaceous geological strata in northeastern China, which were suggested to have parasitized feathered dinosaurs, pterosaurs, and early birds or mammals. In support of these fossils being fleas, a recent publication in BMC Evolutionary Biol...
journal_title:BMC evolutionary biology
pub_type: 信件
doi:10.1186/s12862-015-0568-x
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:In addition to providing phylogenetic relationships, tree making procedures such as parsimony and maximum likelihood can make specific predictions of actual historical sequences. Resurrection of such sequences can be used to understand early events in evolution. In the case of RNA, the nature of parsimony is...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-218
更新日期:2011-07-22 00:00:00
abstract:BACKGROUND:Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a d...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-12-98
更新日期:2012-06-25 00:00:00
abstract:BACKGROUND:Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoi...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-165
更新日期:2008-05-31 00:00:00
abstract:BACKGROUND:One hypothesis for the function of sleep is that it serves as a mechanism to conserve energy. Recent studies have suggested that increased sleep can be an adaptive mechanism to improve survival under food deprivation in Drosophila melanogaster. To test the generality of this hypothesis, we compared sleep and...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-020-01691-8
更新日期:2020-09-22 00:00:00
abstract:BACKGROUND:Analyzing regulation of bacteriophage gene expression historically lead to establishing major paradigms of molecular biology, and may provide important medical applications in the future. Temporal regulation of bacteriophage transcription is commonly analyzed through a labor-intensive combination of biochemi...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-15-S1-S1
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and bi...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-361
更新日期:2011-12-16 00:00:00
abstract::Following publication of the original article. ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12862-018-1321-z
更新日期:2018-12-27 00:00:00
abstract:BACKGROUND:The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1359-6
更新日期:2019-01-23 00:00:00
abstract:BACKGROUND:Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite's phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-014-0180-5
更新日期:2014-08-17 00:00:00
abstract:BACKGROUND:Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and ha...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-228
更新日期:2013-10-18 00:00:00
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
更新日期:2016-06-10 00:00:00
abstract:BACKGROUND:Hymenoptera that mass-provision their offspring have evolved elaborate antimicrobial strategies to ward off fungal infestation of the highly nutritive larval food. Females of the Afro-European Philanthus triangulum and the South American Trachypus elongatus (Crabronidae, Philanthinae) embalm their prey, para...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0565-0
更新日期:2015-12-21 00:00:00
abstract:BACKGROUND:Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, p...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1573-2
更新日期:2020-02-05 00:00:00
abstract:BACKGROUND:Despite the common assumption that multiple mating should in general be favored in males, but not in females, to date there is no consensus on the general impact of multiple mating on female fitness. Notably, very little is known about the genetic and physiological features underlying the female response to ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-014-0239-3
更新日期:2014-11-19 00:00:00