Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events

Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization

Following a duplication, the resulting paralogs tend to diverge. While mutation and natural selection can accelerate this process, they can also slow it. Here, we quantify the paralog homogenization that is caused by point mutations and interlocus gene conversion (IGC). Among 164 duplicated teleost genes, the median percentage of postduplication codon substitutions that arise from IGC rather than point mutation is estimated to be between 7% and 8%. By differentiating between the nonsynonymous codon substitutions that homogenize the protein sequences of paralogs and the nonhomogenizing nonsynonymous substitutions, we estimate the homogenizing nonsynonymous rates to be higher for 163 of the 164 teleost data sets as well as for all 14 data sets of duplicated yeast ribosomal protein-coding genes that we consider. For all 14 yeast data sets, the estimated homogenizing nonsynonymous rates exceed the synonymous rates.

Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

Gene tree-species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of interest in a reference species tree. Such approaches do not account for uncertainty in the gene tree and reconciliation, or do so only heuristically. The effects of these simplifications on the inference of ancient WGDs are unclear. In particular, the effects of variation in gene duplication and loss rates across the species tree have not been considered. Here, we developed a full probabilistic approach for phylogenomic reconciliation-based WGD inference, accounting for both gene tree and reconciliation uncertainty using a method based on the principle of amalgamated likelihood estimation. The model and methods are implemented in a maximum likelihood and Bayesian setting and account for variation of duplication and loss rates across the species tree, using methods inspired by phylogenetic divergence time estimation. We applied our newly developed framework to ancient WGDs in land plants and investigated the effects of duplication and loss rate variation on reconciliation and gene count based assessment of these earlier proposed WGDs.

Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals

BACKGROUND

The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. Three-way and Four-way paralogy regions in human and other vertebrate genomes are considered as vital evidence to support this hypothesis. Alternatively, it has been proposed that such paralogy regions are created by small-scale duplications that occurred at different intervals over the evolution of life.

RESULTS

To address this debate, the present study investigates the evolutionary history of multigene families with at least three-fold representation on human chromosomes 1, 2, 8 and 20. Phylogenetic analysis and the tree topology comparisons classified the members of 36 multigene families into four distinct co-duplicated groups. Gene families falling within the same co-duplicated group might have duplicated together, whereas genes belong to different co-duplicated groups might have distinct evolutionary origins.

CONCLUSION

Taken together with previous investigations, the current study yielded no proof in favor of WGDs hypothesis. Rather, it appears that the vertebrate genome evolved as a result of small-scale duplication events, that cover the entire span of the animals' history.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as ‘chronological reconstruction of ohnolog functions (CHROF)’. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

An insight into the evolutionary history of human MHC paralogon

The vertebrate genome contains several closely spaced sets of paralogous genes from distinct gene families on typically two, three or four different chromosomes (paralogons). These four fold paralogy regions have been considered as historical remnants of whole genome duplication events (WGDs/2R hypothesis). To examine the 2R hypothesis, a robust phylogenetic analysis of 40 multigene families with triplicated or quadruplicated distribution on human MHC bearing chromosomes (1/6/9/19) was conducted. Topology comparison approach categorized the members of 40 families into six distinct co-duplicated groups. Genes belonging to a particular co-duplicated group are duplicated concurrently, whereas genes of two different co-duplicated groups do not share their evolutionary history and have not duplicated in harmony. Our results based on this large scale phylogenetic data set contradict the polyploidization model and are indicative of small-scale duplications and rearrangement events that cover the entire span of animal history.

Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics

Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.

Diversification of four human HOX gene clusters by step-wise evolution rather than ancient whole-genome duplications

HOX genes encode transcriptional factors that play a pivotal role in specifying regional identity in nearly every bilateral animal. The birth of HOX gene cluster and its subsequent evolution, either in regulation or function, underlie the evolution of many bilaterian features and hence to the evolutionary radiation of this group. Despite of this importance, evolution of HOX cluster in vertebrates remains largely obscure because the phylogenetic history of these genes is poorly resolved. This has led to the controversy about whether four HOX clusters in human originated through two rounds (2R) of whole-genome duplications or instead evolved by small-scale events early in vertebrate evolution. Recently, the large-scale phylogenetic analysis of triplicate and quadruplicate paralogous regions residing on human HOX-bearing chromosomes provided an unprecedented insight into events that shaped vertebrate genome early in their history. Based on these data and comparative genomic analysis of fruit fly, red floor beetle, and human, this study infers the genic content of minimal HOX locus in the Urbilaterian and reconstructs its duplication history. It appears that four HOX clusters of humans are not remnants of polyploidy events in vertebrate ancestry. Rather, current evidence suggests that one-to-four transition in HOX cluster number occurred by three-step sequential process involving regional duplication events. Therefore, it is concluded that the evolutionary origin of vertebrate novelties, including the complexity of their body, is the consequence of small-scale genetic changes at widely different times over their history.

Phylogenomic analysis reveals ancient segmental duplications in the human genome

Evolution of organismal complexity and origin of novelties during vertebrate history has been widely explored in context of both regulation of gene expression and gene duplication events. Ohno (1970) for the first time put forward the idea of two rounds whole genome duplication events as the most plausible explanation for evolutionarizing the vertebrate lineage (2R hypothesis). To test the validity of 2R hypothesis, a robust phylogenomic analysis of multigene families with triplicated or quadruplicated representation on human FGFR bearing chromosomes (4/5/8/10) was performed. Topology comparison approach categorized members of 80 families into five distinct co-duplicated groups. Genes belonging to one co-duplicated group are duplicated concurrently, whereas genes of two different co-duplicated groups do not share their duplication history and have not duplicated in congruency. Our findings contradict the 2R model and are indicative of small-scale duplications and rearrangements that cover the entire span of animal's history.

Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution

BACKGROUND

Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history.

RESULTS

Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently.

CONCLUSION

Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life.

Capping protein regulators fine-tune actin assembly dynamics

Capping protein (CP) binds the fast growing barbed end of the actin filament and regulates actin assembly by blocking the addition and loss of actin subunits. Recent studies provide new insights into how CP and barbed-end capping are regulated. Filament elongation factors, such as formins and ENA/VASP (enabled/vasodilator-stimulated phosphoprotein), indirectly regulate CP by competing with CP for binding to the barbed end, whereas other molecules, including V-1 and phospholipids, directly bind to CP and sterically block its interaction with the filament. In addition, a diverse and unrelated group of proteins interact with CP through a conserved 'capping protein interaction' (CPI) motif. These proteins, including CARMIL (capping protein, ARP2/3 and myosin I linker), CD2AP (CD2-associated protein) and the WASH (WASP and SCAR homologue) complex subunit FAM21, recruit CP to specific subcellular locations and modulate its actin-capping activity via allosteric effects.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.

Fourfold paralogy regions on human HOX-bearing chromosomes: role of ancient segmental duplications in the evolution of vertebrate genome

BACKGROUND

Susumu Ohno's idea that modern vertebrates are degenerate polyploids (concept referred as 2R hypothesis) has been the subject of intense debate for past four decades. It was proposed that intra-genomic synteny regions (paralogons) in human genome are remains of ancient polyploidization events that occurred early in the vertebrate history. The quadruplicated paralogon centered on human HOX clusters is taken as evidence that human HOX-bearing chromosomes were structured by two rounds of whole genome duplication (WGD) events.

RESULTS

Evolutionary history of human HOX-bearing chromosomes (chromosomes 2/7/12/17) was evaluated by the phylogenetic analysis of multigene families with triplicated or quadruplicated distribution on these chromosomes. Topology comparison approach categorized the members of 44 families into four distinct co-duplicated groups. Distinct gene families belonging to a particular co-duplicated group, exhibit similar evolutionary history and hence have duplicated simultaneously, whereas genes of two distinct co-duplicated groups do not share their evolutionary history and have not duplicated in concert with each other.

CONCLUSION

The recovery of co-duplicated groups suggests that "ancient segmental duplications and rearrangements" is the most rational model of evolutionary events that have generated the triplicated and quadruplicated paralogy regions seen on the human HOX-bearing chromosomes.

Inference of genome duplications from age distributions revisited

Whole-genome duplications (WGDs), thought to facilitate evolutionary innovations and adaptations, have been uncovered in many phylogenetic lineages. WGDs are frequently inferred from duplicate age distributions, where they manifest themselves as peaks against a small-scale duplication background. However, the interpretation of duplicate age distributions is complicated by the use of K(S), the number of synonymous substitutions per synonymous site, as a proxy for the age of paralogs. Two particular concerns are the stochastic nature of synonymous substitutions leading to increasing uncertainty in K(S) with increasing age since duplication and K(S) saturation caused by the inability of evolutionary models to fully correct for the occurrence of multiple substitutions at the same site. K(S) stochasticity is expected to erode the signal of older WGDs, whereas K(S) saturation may lead to artificial peaks in the distribution. Here, we investigate the consequences of these effects on K(S)-based age distributions and WGD inference by simulating the evolution of duplicated sequences according to predefined real age distributions and re-estimating the corresponding K(S) distributions. We show that, although K(S) estimates can be used for WGD inference far beyond the commonly accepted K(S) threshold of 1, K(S) saturation effects can cause artificial peaks at higher ages. Moreover, K(S) stochasticity and saturation may lead to confounded peaks encompassing multiple WGD events and/or saturation artifacts. We argue that K(S) effects need to be properly accounted for when inferring WGDs from age distributions and that the failure to do so could lead to false inferences.

Phylogenetic history of paralogous gene quartets on human chromosomes 1, 2, 8 and 20 provides no evidence in favor of the vertebrate octoploidy hypothesis

Fourfold paralogy regions in the human genome have been considered historical remnants of whole-genome duplication events predicted to have occurred early in vertebrate evolution. Taking advantage of the well-annotated and high-quality human genomic sequence map as well as the ever-increasing accessibility of large-scale genomic sequence data from a diverse range of animal species, we investigated the prediction that the ancestral vertebrate genome was shaped by two rapid rounds of whole-genome duplication within a period of 10 million years. Both the map self-comparison approach and a phylogenetic analysis revealed that gene families identified as tetralogous on human chromosomes 1/2/8/20 arose by small-scale duplication events that occurred at widely different time points in animal evolution. Furthermore, the data discount the likelihood that tree topologies of the form ((A,B)(C,D)) are best explained by the octoploidy hypothesis. We instead propose that such symmetrical tree patterns are also consistent with local duplications and rearrangement events.

Unraveling ancient segmental duplication events in human genome by phylogenetic analysis of multigene families residing on HOX-cluster paralogons

BACKGROUND

Vertebrate genomes contain extensive intra-genomic conserved synteny, which is the presence of similar set of genes on two or more chromosomes (paralogons). The existence of these paralogons has led to the proposal that vertebrate genome was structured by one or more rounds of ancient whole genome duplications (2R hypothesis).

RESULTS

The 2R hypothesis was tested by phylogenetic analysis of gene families residing on human HOX-bearing chromosomes (HOX-cluster paralogons). These results revealed that, based on their duplication history, 23 gene families with representation on three or four of the human HOX-bearing chromosomes can be partitioned into four discrete co-duplicated groups. The distinct genes within each co-duplicated group share the same evolutionary history and are duplicated in concert with each other, while the constituent genes of two different co-duplicated groups do not share their evolutionary history and are not duplicated simultaneously. These co-duplicated groups are large constituting members from 3 to 8 gene families and suggest that human HOX-cluster paralogons were shaped by ancient segmental duplications (SDs) and rearrangement events that occurred at least as early as before the divergence of bony fishes and tetrapods.

CONCLUSIONS

Based on the recovery of ancient SD events in this analysis and given the widespread evidence in favor of the fact that recent SD events played a pivotal role in changing genome architecture of primates and other recently diverged animals, it is concluded that a more realistic model of ancient vertebrate genome evolutionary history can be deduced by tracing the evolutionary trajectory of the genomes of recently diverged vertebrate species.