Genome duplication and the evolution of conspecific pollen precedence

Conspecific pollen precedence can be a strong reproductive barrier between polyploid and diploid species, but the role of genome multiplication in the evolution of this barrier has not been investigated. Here, we examine the direct effect of genome duplication on the evolution of pollen siring success in tetraploid Chamerion angustifolium. To separate the effects of genome duplication from selection after duplication, we compared pollen siring success of synthesized tetraploids (neotetraploids) with that of naturally occurring tetraploids by applying 2x, 4x (neo or established) or 2x + 4x pollen to diploid and tetraploid flowers. Seed set increased in diploids and decreased in both types of tetraploids as the proportion of pollen from diploid plants increased. Based on offspring ploidy from mixed-ploidy pollinations, pollen of the maternal ploidy always sired the majority of offspring but was strongest in established tetraploids and weakest in neotetraploids. Pollen from established tetraploids had significantly higher siring rates than neotetraploids when deposited on diploid (4x(est) = 47.2%, 4x(neo) = 27.1%) and on tetraploid recipients (4x(est) = 91.9%, 4x(neo) = 56.0%). Siring success of established tetraploids exceeded that of neotetraploids despite having similar pollen production per anther and pollen diameter. Our results suggest that, while pollen precedence can arise in association with the duplication event, the strength of polyploid siring success evolves after the duplication event.     

Gene duplication,genome duplication,and the functional diversification of vertebrate globins

The functional diversification of the vertebrate globin gene superfamily provides an especially vivid illustration of the role of gene duplication and whole-genome duplication in promoting evolutionary innovation. For example, key globin proteins that evolved specialized functions in various aspects of oxidative metabolism and oxygen signaling pathways (hemoglobin [Hb], myoglobin [Mb], and cytoglobin [Cygb]) trace their origins to two whole-genome duplication events in the stem lineage of vertebrates. The retention of the proto-Hb and Mb genes in the ancestor of jawed vertebrates permitted a physiological division of labor between the oxygen-carrier function of Hb and the oxygen-storage function of Mb. In the Hb gene lineage, a subsequent tandem gene duplication gave rise to the proto α- and β-globin genes, which permitted the formation of multimeric Hbs composed of unlike subunits (α₂β₂). The evolution of this heteromeric quaternary structure was central to the emergence of Hb as a specialized oxygen-transport protein because it provided a mechanism for cooperative oxygen-binding and allosteric regulatory control. Subsequent rounds of duplication and divergence have produced diverse repertoires of α- and β-like globin genes that are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different stages of prenatal development and postnatal life. In the ancestor of jawless fishes, the proto Mb and Hb genes appear to have been secondarily lost, and the Cygb homolog evolved a specialized respiratory function in blood-oxygen transport. Phylogenetic and comparative genomic analyses of the vertebrate globin gene superfamily have revealed numerous instances in which paralogous globins have convergently evolved similar expression patterns and/or similar functional specializations in different organismal lineages.     

Genome duplication, divergent resolution and speciation

What are the evolutionary consequences of gene duplication? One answer is speciation, according to a model initially called Reciprocal Silencing and recently expanded and renamed Divergent Resolution. This model shows how the loss of different copies of a duplicated gene in allopatric populations (divergent resolution) can promote speciation by genetically isolating these populations should they become reunited. Genome duplication events produce thousands of duplicated genes. Therefore, lineages with a history of genome duplication might have been especially prone to speciation via divergent resolution.     

Teleost fish with specific genome duplication as unique models of vertebrate evolution

Whole-genome duplication (WGD) is believed to be one of the major evolutionary events that shaped the genome organization of vertebrates. Here, we review recent research on vertebrate genome evolution, specifically on WGD and its consequences for gene and genome evolution in teleost fishes. Recent genome analyses confirmed that all vertebrates experienced two rounds of WGD early in their evolution, and that teleosts experienced a subsequent additional third-round (3R)-WGD. The 3R-WGD was estimated to have occurred 320–400 million years ago in a teleost ancestor, but after its divergence from a common ancestor with living non-teleost actinopterygians (Bichir, Sturgeon, Bowfin, and Gar) based on the analyses of teleost-specific duplicate genes. This 3R-WGD was confirmed by synteny analysis and ancestral karyotype inference using the genome sequences of Tetraodon and medaka. Most of the tetrapods, on the other hand, have not experienced an additional WGD; however, they have experienced repeated chromosomal rearrangements throughout the whole genome. Therefore, different types of chromosomal events have characterized the genomes of teleosts and tetrapods, respectively. The 3R-WGD is useful to investigate the consequences of WGD because it is an evolutionarily recent WGD and thus teleost genomes retain many more WGD-derived duplicates and “traces” of their evolution. In addition, the remarkable morphological, physiological, and ecological diversity of teleosts may facilitate understanding of macrophenotypic evolution on the basis of genetic/genomic information. We highlight the teleosts with 3R-WGD as unique models for future studies on ecology and evolution taking advantage of emerging genomics technologies and systems biology environments.     

Genome duplication and the origin of angiosperms

Despite intensive research, little is known about the origin of the angiosperms and their rise to ecological dominance during the Early Cretaceous. Based on whole-genome analyses of Arabidopsis thaliana, there is compelling evidence that angiosperms underwent two whole-genome duplication events early during their evolutionary history. Recent studies have shown that these events were crucial for the creation of many important developmental and regulatory genes found in extant angiosperm genomes. Here, we argue that these ancient polyploidy events might have also had an important role in the origin and diversification of the angiosperms.     

Genome size and extinction risk in vertebrates

The hypothesis of 'selfish DNA' is tested for the case of animals using the relation between genome size and conservation status of a given species. In contrast to plants, where the larger genome was previously shown to increase the likelihood of extinction, the picture is more complicated in animals. At the within-families and within-orders levels, the larger genome increases the risk of extinction only in reptiles and birds (which have the smallest genomes among tetrapods). In fishes and amphibians, the effect is caused by the higher taxonomic levels (above order). In several phylogenetic lineages of anamniotes, there is a correlation between a higher fraction of threatened species and a lower number of extant species in a lineage with the larger genome. In mammals, no effect was observed at any taxonomic level. The obtained data support the concept of hierarchical selection. It is also shown that, in plants and reptiles, the probability of being threatened increases from less than 10% to more than 80% with the increase in genome size, which can help in establishing conservation priorities.     

Genome size and evolution

Examination of data on genome size for prokaryotic cells suggests an evolutionary scheme.     

Cloning and analysis of an HMG gene from the lamprey Lampetra fluviatilis: gene duplication in vertebrate evolution

Evolution has shaped the organisation of vertebrate genomes, including the human genome. To shed further light on genome history, we have cloned and analysed an HMG gene from lamprey, representing one of the earliest vertebrate lineages. Genes of the HMG1/2 family encode chromosomal proteins that bind DNA in a non-sequence-specific manner, and have been implicated in a variety of cellular processes dependent on chromatin structure. They are characterised by two copies of a conserved motif, the HMG box, followed by an acidic C-terminal region. We report here the cloning of a cDNA clone from the river lamprey Lampetra fluviatilis containing a gene with two HMG boxes and an acidic tail; we designate this gene LfHMG1. Molecular phylogenetic analysis shows that LfHMG1 is descended from a gene ancestral to mammalian HMG1 and HMG2. This implies that there was a duplication event in the HMG1/2 gene family, that occurred after the divergence of the jawed and jawless fishes, 450 million years ago. This conclusion supports and refines the hypothesis that there was a period of extensive gene duplication early in vertebrate evolution. We also show that the HMG1/2 family originated before the protostomes and deuterostomes diverged, over 525 million years ago.     

Understanding vertebrate brain evolution

Four major questions can be asked about vertebrate brain evolution:1) What major changes have occurred in neural organization andfunction? 2) When did these changes occur? 3) By what mechanismsdid these changes occur? 4) Why did these changes occur? Comparativeneurobiologists have been very successful in recognizing majorchanges in brain structure. They have also made progress inunderstanding the functional significance of these changes,although this understanding is primarily limited to sensorycenters, rather than integrative or motor centers, because ofthe relative ease of manipulating the relevant stimuli. Althoughneuropaleontology continues to provide important insights intowhen changes occurred, this approach is generally limited torecognizing variation in overall brain size, and sometimes brainregions, as interpreted from the surface of an endocranial cast.In recent years, most new information regarding when neuralchanges occurred has been based on cladistical analysis of neuralfeatures in extant taxa. Historically, neurobiologists havemade little progress in understanding how and why brains evolve.The emerging field of evolutionary developmental biology appearsto be the most promising approach for revealing how changesin development and its processes produce neural changes, includingthe emergence of novel features. Why neural changes have occurredis the most difficult question and one that has been the mostignored, in large part because its investigation requires abroad interdisciplinary approach involving both behavior andecology.     

On progressive evolution and competitive extinction

Synopsis Extinction may be caused by abiotic and biotic factors in the environment. In the present essay the focus is on extinction caused by biotic factors, and the problem is discussed with reference to two theories of evolution, micromutation and macromutation. According to the former, evolution is adaptive, implying that the only kind of extinction is pseudoextinction or gradual extinction, reflecting the mechanism through which evolution advances in small steps. The macromutation theory asserts that two kinds of evolution exist, divergent (adaptive) and progressive. The latter steadily gives rise to more dominant forms in the phylogenetic hierarchy, and whenever these have a chance to compete with inferior organisms, they will cause the extermination of the latter. However, primitive forms may survive in isolation. The predictions of the macromutation theory are shown to be in better agreement with the fossil record and other observations than are those of the micromutation theory.Invited Editorial