The coevolution of gene family trees

Fryxell, Karl J.

doi:10.1016/s0168-9525(96)80020-5

Cited by 174 publications

(112 citation statements)

References 47 publications

Supporting

Mentioning

103

Contrasting

Unclassified

Order By: Relevance

“…There are recognizable trends of sequence conservation in the different lineages, however, which may reflect changing functional repertoires. Retention of duplicate gene copies, like that observed with AP3 and PI representatives in many species, is often stabilized by the acquisition of novel functions (Fryxell 1996;Cooke et al 1997). The duplicate genes may diverge in such a way that one acquires totally unique functions while the other maintains the ancestral function (Ohno 1970).…”

Section: Phylogenetic Analysismentioning

confidence: 93%

“…Alternatively, the ancestral functions may become partitioned between the two paralogues, resulting in a state of functional complementation that serves to maintain the duplicate copies (Force et al 1999). Examples of these phenomena (and of others) are common in the literature (Fryxell 1996;Force et al 1999;Ganfornina and Sanchez 1999), but it can be difficult to determine exactly how any particular pair of paralogues may be diverging in function.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

See 1 more Smart Citation

Evolution of the Petal and Stamen Developmental Programs: Evidence from Comparative Studies of the Lower Eudicots and Basal Angiosperms

Kramer

Irish

2000

International Journal of Plant Sciences

161

138

View full text Add to dashboard Cite

Section: Phylogenetic Analysismentioning

confidence: 93%

Section: Phylogenetic Analysismentioning

confidence: 99%

Evolution of the Petal and Stamen Developmental Programs: Evidence from Comparative Studies of the Lower Eudicots and Basal Angiosperms

Kramer

Irish

2000

International Journal of Plant Sciences

161

138

View full text Add to dashboard Cite

“…Because there is an intimate association between the ligand and receptor, one might expect that the genes for receptors and hormones should co-evolve, and that new ligandreceptor pairs would evolve from parallel duplications of the hormone and receptor genes [35,36]. However, the evolutionary history of MLNR does not match that of its cognate ligands.…”

Section: Discussionmentioning

confidence: 99%

Gene duplication plays a major role in gene co-option: Studies into the evolution of the motilin/ghrelin family and their receptors

David

Zhang

2011

Chin. Sci. Bull.

View full text Add to dashboard Cite

Extant genes can be modified, or 'tinkered with', to provide new roles or new characteristics of these genes. At the genetic level, this often involves gene duplication and specialization of the resulting genes into particular functions. We investigate how ligand-receptor partnerships evolve after gene duplication. While significant work has been conducted in this area, the examination of additional models should help us better understand the proposed models and potentially reveal novel evolutionary patterns and dynamics. We use bioinformatics, comparative genomics and phylogenetic analyses to show that preproghrelin and prepromotilin descended from a common ancestor and that a gene duplication generated these two genes shortly after the divergence of amphibians and amniotes. The evolutionary history of the receptor family differs from that of their cognate ligands. GPR39 diverges first, and an ancestral receptor gives rise to receptors classified as fish-specific clade A, GHSR and MLNR by successive gene duplications occurring before the divergence of tetrapods and ray-finned fish. The ghrelin/GHSR system is maintained and functionally conserved from fish to mammals. Motilin-MLNR specificity must have arisen by ligand-receptor coevolution after the MLN hormone gene diverged from the GHRL gene in the amniote lineage. Conserved molecular machinery can give rise to new neuroendocrine response mechanisms by the co-option of duplicated genes. Gene duplication is both parsimonious and creative in producing elements for evolutionary tinkering and plays a major role in gene co-option, thus aiding the evolution of greater biological complexity.ghrelin, motilin, gene family, ligand, receptor, coevolution, gene interaction Citation:He J, David I M, Zhang Y P. Gene duplication plays a major role in gene co-option: Studies into the evolution of the motilin/ghrelin family and their receptors.

show abstract

“…Therefore, the corresponding phylogenetic trees should be more similar than those of non-interacting proteins. The first qualitative assessments of this concept were performed with the pairs composed of the insulin and their receptors [91], and dockerins and cohexins [92]. Later, linear correlation between the distance matrices used to construct the trees was proposed to measure tree similarity [93] and the approach was applied to large data sets [94].…”

Section: Discussionmentioning

confidence: 99%

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories

Gómez

Alonso-Allende

Pazos

et al. 2005

Transactions on Computational Systems Biology I

View full text Add to dashboard Cite

Abstract. In recent years there has been an incredible explosion of computational studies of molecular biology systems, particularly those related to the analysis of the structure and organization of molecular networks, as the initial steps toward the possible simulation of the behavior of simple cellular systems. Needless to say, this task will not be possible without the availability of a new class of data derived from experimental proteomics. Large-scale application of the yeast two-hybrid system, affinity purification (TAPs-MS), and other methodologies are for the first time providing overviews of complete protein interaction networks. Interestingly a number of computational methods are also contributing substantially to the identification of protein interactions, by comparing genome organization and evolution. Other disciplines, such as structural biology and computational structural biology, are complementing the information on interaction networks by providing detailed molecular descriptions of the corresponding complexes, which will become essential for the direct manipulation of the networks using theoretical or experimental methods. The storage, manipulation and visualization of the huge volumes of information about protein interactions and networks pose similar problems, irrespective of the source of the information: experimental or computational. In this sense, a number of competing systems and emerging standards have appeared in parallel with the publication of the data. In this review, we will provide an overview of the main experimental, high-throughput methods for the study of protein interactions, the parallel developments of computational methods for the prediction of protein interactions based on genome and sequence information, and the development of databases and standards that facilitate the analysis of all this information.

show abstract

The coevolution of gene family trees

Cited by 174 publications

References 47 publications

Evolution of the Petal and Stamen Developmental Programs: Evidence from Comparative Studies of the Lower Eudicots and Basal Angiosperms

Evolution of the Petal and Stamen Developmental Programs: Evidence from Comparative Studies of the Lower Eudicots and Basal Angiosperms

Gene duplication plays a major role in gene co-option: Studies into the evolution of the motilin/ghrelin family and their receptors

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories

Contact Info

Product

Resources

About