scholarly journals New genes from old: asymmetric divergence of gene duplicates and the evolution of development

2017 ◽  
Vol 372 (1713) ◽  
pp. 20150480 ◽  
Author(s):  
Peter W. H. Holland ◽  
Ferdinand Marlétaz ◽  
Ignacio Maeso ◽  
Thomas L. Dunwell ◽  
Jordi Paps
Keyword(s):  
Gene Duplication ◽  
Homeobox Genes ◽  
Morphological Diversity ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Sequence Change ◽  
New Genes ◽  
Gene Duplicates ◽  
Evo Devo ◽  
Animal Genomes

Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such ‘asymmetric evolution’ seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

scholarly journals The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants ◽  
2016 ◽  
Vol 2 (11) ◽  
Author(s):  
Xiangchao Gan ◽  
Angela Hay ◽  
Michiel Kwantes ◽  
Georg Haberer ◽  
Asis Hallab ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Human Genetics ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Close Relative ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Genome Wide ◽  
Differential Gene

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

Patterns of Gene Duplication and Functional Evolution During the Diversification of the AGAMOUS Subfamily of MADS Box Genes in Angiosperms

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 1011-1023
Author(s):  
Elena M Kramer ◽  
M Alejandra Jaramillo ◽  
Verónica S Di Stilio
Keyword(s):  
Gene Duplication ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Morphological Diversity ◽  
Reproductive Organs ◽  
Gene Duplications ◽  
Mads Box ◽  
Mads Box Genes ◽  
Data Set ◽  
Angiosperm Species

Abstract Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG -like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity.

scholarly journals Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes

2001 ◽  
Vol 11 (4) ◽  
pp. 555-565 ◽  
Author(s):  
I. King Jordan ◽  
Kira S. Makarova ◽  
John L. Spouge ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Duplication ◽  
Average Score ◽  
Specific Gene ◽  
Tandem Gene Duplication ◽  
New Genes ◽  
A Genome ◽  
Prokaryotic Genomes ◽  
Bacterial Chromosomes ◽  
Large Clusters ◽  
Lineage Specific Gene

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (∼5%–33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size ≥20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.

scholarly journals Evolution of Antennapedia-Class Homeobox Genes

Genetics ◽  
1996 ◽  
Vol 142 (1) ◽  
pp. 295-303 ◽  
Author(s):  
Jianzhi Zhang ◽  
Masatoshi Nei
Keyword(s):  
Gene Expression ◽  
Homeobox Genes ◽  
Amino Acid Sequences ◽  
Gene Arrangement ◽  
Gene Duplications ◽  
Group I ◽  
Group 3 ◽  
Group Ii ◽  
Anterior Posterior

Antennapedia (Antp)-class homeobox genes are involved in the determination of pattern formation along the anterior-posterior axis of the animal embryo. A phylogenetic analysis of Antp-class homeodomains of the nematode, Drosophila, amphioxus, mouse, and human indicates that the 13 cognate group genes of this gene family can be divided into two major groups, i.e., groups I and II. Group I genes can further be divided into subgroups A (cognate groups 1–2), B (cognate group 3), and C (cognate groups 4–8), and group II genes can be divided into subgroups D (cognate groups 9–10) and E (cognate groups 11–13), though this classification is somewhat ambiguous. Evolutionary distances among different amino acid sequences suggest that the divergence between group I and group II genes occurred ∼1000 million years (MY) ago, and the five different subgroups were formed by ∼600 MY ago, probably before the divergence of Pseudocoelomates (e.g., nematodes) and Coelomates (e.g., insects and chordates). Our results show that the genes that are phylogenetically close are also closely located in the chromosome, suggesting that the colinearity between the gene expression and gene arrangement was generated by successive tandem gene duplications and that the gene arrangement has been maintained by some sort of selection.

scholarly journals Origin of animal multicellularity: precursors, causes, consequences—the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion

2017 ◽  
Vol 372 (1713) ◽  
pp. 20150476 ◽  
Author(s):  
Thomas Cavalier-Smith
Keyword(s):  
Connective Tissue ◽  
Photosynthetic Bacteria ◽  
Cell Structure ◽  
Morphological Diversity ◽  
Cambrian Explosion ◽  
Feeding Modes ◽  
Selection For ◽  
Evo Devo ◽  
Gastraea Theory ◽  
Bacterial Food

Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

scholarly journals Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes

2001 ◽  
Vol 11 (5) ◽  
pp. 771-780 ◽  
Author(s):  
Austin L. Hughes ◽  
Jack da Silva ◽  
Robert Friedman
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Gene Duplications ◽  
Human Chromosomes ◽  
Time Period ◽  
Genome Duplications

The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the fourHox-bearing chromosomes (the chromosomes bearing theHox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the humanHox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hoxclusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.

scholarly journals Major evolutionary transitions and innovations: the tympanic middle ear

2017 ◽  
Vol 372 (1713) ◽  
pp. 20150483 ◽  
Author(s):  
Abigail S. Tucker
Keyword(s):  
Middle Ear ◽  
Morphological Diversity ◽  
The Novel ◽  
Evolutionary Transitions ◽  
Jaw Joint ◽  
Evolution Of Mammals ◽  
Key Steps ◽  
Evo Devo ◽  
Relationship Of ◽  
The Relationship

One of the most amazing transitions and innovations during the evolution of mammals was the formation of a novel jaw joint and the incorporation of the original jaw joint into the middle ear to create the unique mammalian three bone/ossicle ear. In this review, we look at the key steps that led to this change and other unusual features of the middle ear and how developmental biology has been providing an understanding of the mechanisms involved. This starts with an overview of the tympanic (air-filled) middle ear, and how the ear drum (tympanic membrane) and the cavity itself form during development in amniotes. This is followed by an investigation of how the ear is connected to the pharynx and the relationship of the ear to the bony bulla in which it sits. Finally, the novel mammalian jaw joint and versatile dentary bone will be discussed with respect to evolution of the mammalian middle ear. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

Distal-less-related homeobox genes of vertebrates: Evolution, function, and regulation

2000 ◽  
Vol 78 (5) ◽  
pp. 593-601 ◽  
Author(s):  
Ted Zerucha ◽  
Marc Ekker
Keyword(s):  
Homeobox Genes ◽  
Gene Families ◽  
Duplication Event ◽  
Developmental Expression ◽  
Gene Clustering ◽  
Tandem Gene Duplication ◽  
Current State ◽  
Branchial Arches ◽  
Genomic Scale ◽  
Dlx Genes

Homeobox genes of the Distal-less family have been identified in virtually all metazoan groups where they play roles in the ontogeny of these animals. The vertebrate Distal-less related genes (Dlx genes) are thought to have arisen as a result of a tandem gene duplication event followed by a number of larger genomic scale duplications and thus represent an interesting model with which to study the evolution of clustered gene families. Dlx genes are involved in the development of the forebrain, branchial arches, sensory organs, and limbs. Here we describe the current state of knowledge of the Dlx genes in terms of their developmental expression, how this expression is regulated and how the products of these genes function, once expressed. We highlight a number of recent studies that have shed light on the transcriptional regulation of this gene family. These findings have not only contributed to our understanding of the selective pressures involved in the maintenance of familial gene clustering in genomes, but also to our understanding of how genes may diverge in function during the course of evolution as a result of divergence of regulatory mechanisms.Key words: genome, homeodomain, inner ear, olfactory placode, transcription.

scholarly journals Evo-devo and accounting for Darwin's endless forms

2011 ◽  
Vol 366 (1574) ◽  
pp. 2069-2075 ◽  
Author(s):  
Paul M. Brakefield
Keyword(s):  
Natural Selection ◽  
Common Ancestry ◽  
Developmental Constraints ◽  
Evolutionary Diversification ◽  
New Genes ◽  
The Earth ◽  
Regulatory Machinery ◽  
Evo Devo ◽  
Opening Up ◽  
Trait Space

Evo-devo has led to dramatic advances in our understanding of how the processes of development can contribute to explaining patterns of evolutionary diversification that underlie the endless forms of animal life on the Earth. This is increasingly the case not only for the origins of evolutionary novelties that permit new functions and open up new adaptive zones, but also for the processes of evolutionary tinkering that occur within the subsequent radiations of related species. Evo-devo has time and again yielded spectacular examples of Darwin's notions of common ancestry and of descent with modification. It has also shown that the evolution of endless forms is more about the evolution of the regulatory machinery of ancient genes than the origin and elaboration of new genes. Evolvability, especially with respect to the capacity of a developmental system to evolve and to generate the variation in form for natural selection to screen, has become a pivotal focus of evo-devo. As a consequence, a balancing of the concept of endless forms in morphospace with a greater awareness of the potential for developmental constraints and bias is becoming more general. The prospect of parallel horizons opening up for the evolution of behaviour is exciting; in particular, does Sean Carroll's phrase referring to old genes learning new tricks in the evolution of endless forms apply equally as well to patterns of diversity and disparity in behavioural trait-space?

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