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 metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. RESULTS:We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. CONCLUSIONS:The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.
journal_name
BMC Evol Bioljournal_title
BMC evolutionary biologyauthors
Bernhardsson S,Gerlee P,Lizana Ldoi
10.1186/1471-2148-11-20subject
Has Abstractpub_date
2011-01-20 00:00:00pages
20issn
1471-2148pii
1471-2148-11-20journal_volume
11pub_type
杂志文章abstract:BACKGROUND:Evolutionary histories of glutamyl-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) in bacteria are convoluted. After the divergence of eubacteria and eukarya, bacterial GluRS glutamylated both tRNAGln and tRNAGlu until GlnRS appeared by horizontal gene transfer (HGT) from eukaryotes or a dupli...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-26
更新日期:2014-02-12 00:00:00
abstract:BACKGROUND:Many pathologies that modify the shell geometry and ornamentation of ammonoids are known from the fossil record. Since they may reflect the developmental response of the organism to a perturbation (usually a sublethal injury), their study is essential for exploring the developmental mechanisms of these extin...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1538-5
更新日期:2019-11-13 00:00:00
abstract:BACKGROUND:Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccat...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-5-57
更新日期:2005-10-20 00:00:00
abstract:BACKGROUND:Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fe...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-82
更新日期:2014-04-17 00:00:00
abstract:BACKGROUND:Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local dive...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-150
更新日期:2008-05-16 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: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:In gnathostomes, chemosensory receptors (CR) expressed in olfactory epithelia are encoded by evolutionarily dynamic gene families encoding odorant receptors (OR), trace amine-associated receptors (TAAR), V1Rs and V2Rs. A limited number of OR-like sequences have been found in invertebrate chordate genomes. Wh...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-180
更新日期:2009-07-31 00:00:00
abstract:BACKGROUND:Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this st...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-273
更新日期:2013-12-17 00:00:00
abstract:BACKGROUND:PHOSPHATE1 (PHO1) gene family members have diverse roles in plant growth and development, and they have been studied in Arabidopsis, rice, and Physcomitrella. However, it has yet to be described in other plants. Therefore, we surveyed the evolutionary patterns of genomes within the plant PHO1 gene family, fo...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-103
更新日期:2013-05-24 00:00:00
abstract:BACKGROUND:The existence of "ancient asexuals", taxa that have persisted for long periods of evolutionary history without sexual recombination, is both controversial and important for our understanding of the evolution and maintenance of sexual reproduction. A lack of sex has consequences not only for the ecology of th...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-8-194
更新日期:2008-07-07 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: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:Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to re...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0649-5
更新日期:2016-04-14 00:00:00
abstract:BACKGROUND:Recently we proposed an evolutionary explanation for a spinal pathology that afflicts many people, intervertebral disc herniation (Plomp et al. [2015] BMC Evolutionary Biology 15, 68). Using 2D data, we found that the bodies and pedicles of lower vertebrae of pathological humans were more similar in shape to...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-019-1550-9
更新日期:2019-12-16 00:00:00
abstract:BACKGROUND:Hotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a majo...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-155
更新日期:2013-08-19 00:00:00
abstract:BACKGROUND:In most species, males compete to gain both matings (via pre-copulatory competition) and fertilizations (via post-copulatory competition) to maximize their reproductive success. However, the quantity of resources devoted to sexual traits is finite, and so males are predicted to balance their investment betwe...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-14-79
更新日期:2014-04-10 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:Bacterial global regulators each regulate the expression of several hundred genes. In Escherichia coli, the top seven global regulators together control over half of all genes. Leucine-responsive regulatory protein (Lrp) is one of these top seven global regulators. Lrp orthologs are very widely distributed, ...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-016-0685-1
更新日期:2016-05-20 00:00:00
abstract:BACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp)...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-107
更新日期:2013-05-29 00:00:00
abstract:BACKGROUND:Lymnaeidae snails play a prominent role in the transmission of helminths, mainly trematodes of medical and veterinary importance (e.g., Fasciola liver flukes). As this family exhibits a great diversity in shell morphology but extremely homogeneous anatomical traits, the systematics of Lymnaeidae has long bee...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-10-381
更新日期:2010-12-09 00:00:00
abstract:BACKGROUND:The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The ability to control sophisticated gene expression patterns enabled these ancient organisms to evolve sev...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-37
更新日期:2013-02-11 00:00:00
abstract:BACKGROUND:Maternal care (egg-nymph guarding behavior) has been recorded in some genera of Acanthosomatidae. However, the origin of the maternal care in the family has remained unclear due to the lack of phylogenetic hypotheses. Another reproductive mode is found in non-caring species whose females smear their eggs bef...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/s12862-015-0537-4
更新日期:2015-11-19 00:00:00
abstract:BACKGROUND:Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assume...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-11-299
更新日期:2011-10-12 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:BMC evolutionary biology
pub_type: 已发布勘误
doi:10.1186/s12862-020-01686-5
更新日期:2020-10-07 00:00:00
abstract:BACKGROUND:Rodent and primate pregnancy-specific glycoprotein (PSG) gene families have expanded independently from a common ancestor and are expressed virtually exclusively in placental trophoblasts. However, within each species, it is unknown whether multiple paralogs have been selected for diversification of function...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-5-39
更新日期:2005-06-29 00:00:00
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 relation...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-13-120
更新日期:2013-06-11 00:00:00
abstract:BACKGROUND:Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropic...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-250
更新日期:2009-10-14 00:00:00
abstract:BACKGROUND:The coral skeleton consists of CaCO3 deposited upon an organic matrix primarily as aragonite. Currently galaxin, from Galaxea fascicularis, is the only soluble protein component of the organic matrix that has been characterized from a coral. Three genes related to galaxin were identified in the coral Acropor...
journal_title:BMC evolutionary biology
pub_type: 杂志文章
doi:10.1186/1471-2148-9-178
更新日期:2009-07-29 00:00:00
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
更新日期:2011-05-28 00:00:00