https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow (1996, p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh (1995, p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff (1997, p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. (1997, p. 362)

https://www.genetics.org/content/genetics/151/4/1531.full.pdf

Preservation of Duplicate Genes by Complementary, Degenerative Mutations

▪ Abstract Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immed...

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Polyploid Incidence and Evolution

Polyploidy is widely acknowledged as a major mechanism of adaptation and speciation in plants. The stages in polyploid evolution include frequent fertility bottlenecks and infrequent events such as gametic nonreduction and interspecific hybridization, yet little is known about how these and other factors influence overall rates of polyploid formation. Here we review the literature regarding polyploid origins, and quantify parameter values for each of the steps involved in the principal pathways. In contrast to the common claim that triploids are sterile, our results indicate that the triploid bridge pathway can contribute significantly to autopolyploid formation regardless of the mating system, and to allopolyploid formation in outcrossing taxa. We estimate that the total rate of autotetraploid formation is of the same order as the genic mutation rate (10 i5 ), and that a high frequency of interspecific hybridization (0.2% for selfing taxa, 2.7% for outcrossing taxa) is required for the rate of tetraploid formation via allopolyploidy to equal that by autopolyploidy. We conclude that the rate of autopolyploid formation may often be higher than the rate of allopolyploid formation. Further progress toward understanding polyploid origins requires studies in natural populations that quantify: (a) the frequency of unreduced gametes, (b) the effectiveness of triploid bridge pathways, and (c) the rates of interspecific hybridization.

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Pathways, mechanisms, and rates of polyploid formation in flowering plants

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

/pdf/genome-evolution-in-polyploids-eeag8xqgqu.pdf

Genome evolution in polyploids

I. Polyploidy in Plant Evolution.- Origins of Polyploids.- Cytogenetics of Polyploids.- Polyploidy and Distribution.- Physiology of Polyploids.- Chemistry of Polyploids.- Polyploidy in Species Populations.- Polyploidy in Plant Evolution: Summary.- II. Polyploidy in Plant Taxa.- Polyploidy in Algae.- Polyploidy in Fungi.- Polyploidy in Bryophytes with Special Emphasis on Mosses.- Polyploidy in Pteridophytes.- Polyploidy in Gymnosperms.- Polyploidy in Angiosperms: Monocotyledons.- Polyploidy in Angiosperms: Dicotyledons.- Polyploidy in Plant Taxa: Summary.- III. Polyploidy in Animal Evolution.- Polyploidy in Insect Evolution.- Role of Polyploidy in the Evolution of Fishes.- Evolutionary Significance of Polyploidy in Amphibians and Reptiles.- Polyploidy In Animal Evolution: Summary.- IV. Polyploidy and Agriculture.- Polyploidy and Plant Domestication.- Problems of AlloPolyploidy in Triticale.- Uses of Wheat Aneuploids.- Some Applications and Misapplications of Induced Polyploidy to Plant Breeding.- Maximizing Heterozygosity in Autopolyploids.- Polyploidy and Agriculture: Summary.- V. Polyploidy: Future Prospects.- Polyploidy in Plants: Unsolved Problems and Prospects.- Workshop Reports.- Polyploidy, Plants, and Electrophoresis.- Molecular Techniques Applied to Polyploids.- Principles of Demographic Analysis Applied to Natural Polyploid Populations.- Newly Attained Polyploidy and/or Clonal Reproduction in Animals: The Brink of Extinction or Threshold to New Frontiers?.- Cytogenetics and Crop Improvement.- Conference Participants.- List of Contributors.- Index to Names of Organisms.

Polyploidy : biological relevance

Polyploidy in populations of well-differentiated plant species is now widely recognized (1,2). Most reports, however, are limited to a few individuals from one or several populations and thereby illustrate only a fraction of the extant genomic diversity in most species. They rarely purport populational dynamics involving Polyploidy as an evolutionary process. Nevertheless, there are recent notable exceptions and these will be utilized freely in this review of Polyploidy within species populations.

Polyploidy in species populations.

Natural antimycobacterial metabolites: current status.

This study investigates the impact of hybridization and polyploidy in the evolution of eastern North American roses. We explore these processes in the Rosa carolina complex (section Cinnamomeae), which consists of five diploid and three tetraploid species. To clarify the status and origins of polyploids, a haplotype network (statistical parsimony) of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) nuclear gene was estimated for polyploids of the complex and for diploids of section Cinnamomeae in North America. A genealogical approach helped to decipher the evolutionary history of polyploids from noise created by hybridization, incomplete lineage sorting, and allelic segregation. At the diploid level, species west of the Rocky Mountains are distinct from eastern species. In the east, two groups of diploids were found: one consists of R. blanda and R. woodsii and the other of R. foliolosa, R. nitida, and R. palustris. Only eastern diploids are involved in the origins of the polyploids. Rosa arkansana is derived from the blanda-woodsii group, R. virginiana originated from the foliolosa-nitida-palustris group, and R. carolina is derived from a hybrid between the two diploid groups. The distinct origins of these polyploid taxa support the hypothesis that the three polyploids are separate species.

Walter H. Lewis

Papers

Polyploidy : biological relevance

Polyploidy in species populations.

Natural antimycobacterial metabolites: current status.

Polyploid and hybrid evolution in roses east of the Rocky Mountains

Cytopalynological Study of African Hedyotideae (Rubiaceae)