scholarly journals The Role of Reticulate Evolution in Creating Innovation and Complexity

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kristen S. Swithers ◽  
Shannon M. Soucy ◽  
J. Peter Gogarten
Keyword(s):  
Metabolic Pathways ◽  
Driving Forces ◽  
Reticulate Evolution ◽  
Neutral Evolution ◽  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
New Host ◽  
Whole Genome Duplications ◽  
Genome Duplications

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.

scholarly journals Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe

2020 ◽  
Author(s):  
Xinyi Guo ◽  
Terezie Mandáková ◽  
Karolína Trachtová ◽  
Barış Özüdoğru ◽  
Jianquan Liu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Reticulate Evolution ◽  
Land Plant ◽  
Whole Genome ◽  
Plant Family ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
History Of ◽  
Single Genus ◽  
Genomic Relatedness

Abstract Pervasive hybridization and whole genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. While frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (c. 60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring post-polyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

scholarly journals Global patterns and rates of habitat transitions across the eukaryotic tree of life

2021 ◽  
Author(s):  
Mahwash Jamy ◽  
Charlie Biwer ◽  
Daniel Vaulot ◽  
Aleix Obiol ◽  
Hongmei Jing ◽  
...  
Keyword(s):  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
Short Read ◽  
Evolution Of Life ◽  
Long Read ◽  
Saline Habitats ◽  
Global Patterns ◽  
Almost All ◽  
New Habitats

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.

scholarly journals Cause and consequences of genome duplication in haploid yeast populations

2018 ◽  
Author(s):  
Kaitlin J. Fisher ◽  
Sean W. Buskirk ◽  
Ryan C. Vignogna ◽  
Daniel A. Marad ◽  
Gregory I. Lang
Keyword(s):  
Genome Duplication ◽  
Neutral Evolution ◽  
Phenotypic Evolution ◽  
Deleterious Mutations ◽  
Structural Variants ◽  
Laboratory Evolution ◽  
Fitness Advantage ◽  
Whole Genome Duplications ◽  
Genome Duplications

ABSTRACTWhole genome duplications (WGD) represent important evolutionary events that shape future adaptation. WGDs are known to have occurred in the lineages leading to plants, fungi, and vertebrates. Changes to ploidy level impact the rate and spectrum of beneficial mutations and thus the rate of adaptation. Laboratory evolution experiments initiated with haploid Saccharomyces cerevisiae cultures repeatedly experience WGD. We report recurrent genome duplication in 46 haploid yeast populations evolved for 4,000 generations. We find that WGD confers a fitness advantage, and this immediate fitness gain is accompanied by a shift in genomic and phenotypic evolution. The presence of ploidy-enriched targets of selection and structural variants reveals that autodiploids utilize adaptive paths inaccessible to haploids. We find that autodiploids accumulate recessive deleterious mutations, indicating an increased capacity for neutral evolution. Finally, we report that WGD results in a reduced adaptation rate, indicating a trade-off between immediate fitness gains and long term adaptability.

scholarly journals Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

2020 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Henry Barton ◽  
Victoria Pritchard ◽  
Craig Primmer
Keyword(s):  
Atlantic Salmon ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Regulatory Elements ◽  
Functional Redundancy ◽  
Neutral Evolution ◽  
Whole Genome ◽  
Regulatory Evolution ◽  
Whole Genome Duplications ◽  
Genome Duplications

AbstractWhole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained asymmetric regulatory evolution. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.Significance statementRegulatory evolution following whole genome duplications (WGD) has been investigated at the gene expression level, but studies of the regulatory elements that control expression have been lacking. By investigating regulatory elements in the Atlantic salmon genome, which has undergone a whole genome duplication 100-80 million years ago, we discovered patterns suggesting that neutral divergence is the prevalent mode of regulatory element evolution post-WGD. Our results suggest mechanisms for explaining the prevalence of asymmetric gene expression evolution following whole genome duplication, as well as the mismatch between evolutionary rates in enhancers versus that of promoters.

scholarly journals Vertebrate whole genome duplications shaped the current 3D genome architecture

2021 ◽  
Author(s):  
Caelinn James ◽  
Marco Trevisan-Herraz ◽  
Daniel Rico
Keyword(s):  
Regulatory Networks ◽  
Whole Genome ◽  
3D Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Topologically Associated Domains ◽  
Major Transition ◽  
Evolution Of Gene Regulation ◽  
Evolutionary Success

Topologically associated domains (TADs) are interaction sub-networks of 3D genomes. TAD boundaries frequently coincide with genome breaks while their deletion is under negative selection, suggesting that TADs act as modules facilitating genome rearrangements and metazoan evolution. However, the role of TADs in the evolution of gene regulation and essentiality is not well understood. Here, we show that TADs play a role organising ancestral functions and evolutionary novelty. We discovered that genes co-localise by evolutionary age in the human and mouse genomes, resulting in TADs that have different proportions of younger and older genes. A major transition in the TAD age co-localisation patterns is observed between the genes born as a result of the vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also found that primate- and rodent-specific genes are more frequently essential when they are located in 'aged' TADs and connected to genes that have not duplicated since the WGD. Our data suggests that evolutionary success of recent genes may increase when located in functionally relevant TADs with established regulatory networks.

scholarly journals Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors

2015 ◽  
Author(s):  
Núria Radó-Trilla ◽  
Krisztina Arató ◽  
Cinta Pegueroles ◽  
Alicia Raya ◽  
Susana de la Luna ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Driving Forces ◽  
Gene Families ◽  
Low Complexity ◽  
Individual Gene ◽  
Genome Duplications ◽  
The Individual ◽  
Tf Gene

The high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families (107 out of 237) originated during the 2R-WGD contain LCRs, compared to only a small percentage of the non-duplicated TF genes used as a control (15 out of 115). At the individual gene level, we observe that twice as many duplicated TFs have gained LCRs as non-duplicated TFs. In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

Evolution of Glucosinolate Diversity via Whole-Genome Duplications, Gene Rearrangements, and Substrate Promiscuity

2019 ◽  
Vol 70 (1) ◽  
pp. 585-604 ◽  
Author(s):  
Brenden Barco ◽  
Nicole K. Clay
Keyword(s):  
Protein Function ◽  
Higher Plants ◽  
Gene Rearrangements ◽  
Biosynthetic Enzymes ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Repeated Evolution ◽  
Substrate Promiscuity

Over several decades, glucosinolates have become a model system for the study of specialized metabolic diversity in plants. The near-complete identification of biosynthetic enzymes, regulators, and transporters has provided support for the role of gene duplication and subsequent changes in gene expression, protein function, and substrate specificity as the evolutionary bases of glucosinolate diversity. Here, we provide examples of how whole-genome duplications, gene rearrangements, and substrate promiscuity potentiated the evolution of glucosinolate biosynthetic enzymes, regulators, and transporters by natural selection. This in turn may have led to the repeated evolution of glucosinolate metabolism and diversity in higher plants.

Chronic Pain: Fundamental Scientific Considerations, Specifically for Legal Claims

2013 ◽  
Vol 18 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Robert J. Barth
Keyword(s):  
Health Outcomes ◽  
Pain Perception ◽  
Driving Forces ◽  
Psychological Treatment ◽  
Dominant Role ◽  
Meta Analysis ◽  
General Medicine ◽  
Pain Syndrome ◽  
Problematic Relationship

Abstract Scientific findings have indicated that psychological and social factors are the driving forces behind most chronic benign pain presentations, especially in a claim context, and are relevant to at least three of the AMA Guides publications: AMA Guides to Evaluation of Disease and Injury Causation, AMA Guides to Work Ability and Return to Work, and AMA Guides to the Evaluation of Permanent Impairment. The author reviews and summarizes studies that have identified the dominant role of financial, psychological, and other non–general medicine factors in patients who report low back pain. For example, one meta-analysis found that compensation results in an increase in pain perception and a reduction in the ability to benefit from medical and psychological treatment. Other studies have found a correlation between the level of compensation and health outcomes (greater compensation is associated with worse outcomes), and legal systems that discourage compensation for pain produce better health outcomes. One study found that, among persons with carpal tunnel syndrome, claimants had worse outcomes than nonclaimants despite receiving more treatment; another examined the problematic relationship between complex regional pain syndrome (CRPS) and compensation and found that cases of CRPS are dominated by legal claims, a disparity that highlights the dominant role of compensation. Workers’ compensation claimants are almost never evaluated for personality disorders or mental illness. The article concludes with recommendations that evaluators can consider in individual cases.

Convergence of Corporate Governance Models

2004 ◽  
pp. 129-140 ◽  
Author(s):  
M. Tretyakov
Keyword(s):  
Corporate Governance ◽  
Institutional Environment ◽  
Driving Forces ◽  
Commodity Markets ◽  
Legal Systems ◽  
National Institutions ◽  
Governance Models ◽  
Changing Role

The article focuses on the analysis of the process of convergence of outsider and insider models of corporate governance. Chief characteristics of basic and intermediate systems of corporate governance as well as the changing role of its main agents are under examination. Globalization of financial and commodity markets, convergence of legal systems, an open exchange of ideas and information are the driving forces of the convergence of basic systems of corporate governance. However the convergence does not imply the unification of institutional environment and national institutions of corporate governance.

The Incentives to, and Constraints upon, Product Innovation

2018 ◽  
Author(s):  
Paul Stoneman ◽  
Eleonora Bartoloni ◽  
Maurizio Baussola
Keyword(s):  
Survey Data ◽  
Product Innovation ◽  
Product Space ◽  
Driving Forces ◽  
Product Line ◽  
Decision Uncertainty ◽  
Market Structures ◽  
Product Innovations

This chapter explores the factors that affect the firm’s decision to undertake product innovation. The discussion encompasses the driving forces that encourage product innovation, for example innovation by others or the ageing of an existing product line; however, the basic rationale is the search for profits. The chapter also addresses decisions about: the extent of innovation in general; horizontal and vertical product innovations separately; and the location of innovations in product space. The role of market structures in the product innovation decision, uncertainty in the innovating environment, and issues relating to emulation and copying are also addressed. Constraints to product innovation that survey data indicate are most important—innovation costs, risk and finance, and the availability of qualified labour—are also addressed.

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