Mutation rate variation in eukaryotes: evolutionary implications of site-specific mechanisms

Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems

What is an organism? In the absence of a fundamental biological definition, what constitutes a living organism, whether it is a unicellular microbe, a multicellular being or a multi-organismal society, remains an open question. New models of living systems are needed to address the scale of this question, with implications for the relationship between humanity and planetary ecology. Here we develop a generic model of an organism that can be applied across multiple scales and through major evolutionary transitions to form a toolkit, or bio-organon, for theoretical studies of planetary-wide physiology. The tool identifies the following core organismic principles that cut across spatial scale: (1) evolvability through self-knowledge, (2) entanglement between energy and information, and (3) extrasomatic "technology" to scaffold increases in spatial scale. Living systems are generally defined by their ability to self-sustain against entropic forces of degradation. Life "knows" how to survive from the inside, not from its genetic code alone, but by utilizing this code through dynamically embodied and functionally specialized flows of information and energy. That is, entangled metabolic and communication networks bring encoded knowledge to life in order to sustain life. However, knowledge is itself evolved and is evolving. The functional coupling between knowledge, energy and information has ancient origins, enabling the original, cellular "biotechnology," and cumulative evolutionary creativity in biochemical products and forms. Cellular biotechnology also enabled the nesting of specialized cells into multicellular organisms. This nested organismal hierarchy can be extended further, suggesting that an organism of organisms, or a human "superorganism," is not only possible, but in keeping with evolutionary trends.

Unknown to Known: Advancing Knowledge of Coral Gene Function

Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function.

Tandem amino acid repeats in the green anole (Anolis carolinensis) and other squamates may have a role in increasing genetic variability

Background

Tandem amino acid repeats are characterised by the consecutive recurrence of a single amino acid. They exhibit high rates of length mutations in addition to point mutations and have been proposed to be involved in genetic plasticity. Squamate reptiles (lizards and snakes) diversify in both morphology and physiology. The underlying mechanism is yet to be understood. In a previous phylogenomic analysis of reptiles, the density of tandem repeats in an anole lizard diverged heavily from that of the other reptiles. To gain further insight into the tandem amino acid repeats in squamates, we analysed the repeat content in the green anole (Anolis carolinensis) proteome and compared the amino acid repeats in a large orthologous protein data set from six vertebrates (the Western clawed frog, the green anole, the Chinese softshell turtle, the zebra finch, mouse and human).

Results

Our results revealed that the number of amino acid repeats in the green anole exceeded those found in the other five species studied. Species-only repeats were found in high proportion in the green anole but not in the other five species, suggesting that the green anole had gained many amino acid repeats in either the Anolis or the squamate lineage. Since the amino acid repeat containing genes in the green anole were highly enriched in genes related to transcription and development, an important family of developmental genes, i.e., the Hox family, was further studied in a wide collection of squamates. Abundant amino acid repeats were also observed, implying the general high tolerance of amino acid repeats in squamates. A particular enrichment of amino acid repeats was observed in the central class Hox genes that are known to be responsible for defining cervical to lumbar regions.

Conclusions

Our study suggests that the abundant amino acid repeats in the green anole, and possibly in other squamates, may play a role in increasing the genetic variability, and contribute to the evolutionary diversity of this clade.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2430-y) contains supplementary material, which is available to authorized users.

The genome as a developmental organ

This paper applies the conceptual toolkit of Evolutionary Developmental Biology (evo-devo) to the evolution of the genome and the role of the genome in organism development. This challenges both the Modern Evolutionary Synthesis, the dominant view in evolutionary theory for much of the 20th century, and the typically unreflective analysis of heredity by evo-devo. First, the history of the marginalization of applying system-thinking to the genome is described. Next, the suggested framework is presented. Finally, its application to the evolution of genome modularity, the evolution of induced mutations, the junk DNA versus ENCODE debate, the role of drift in genome evolution, and the relationship between genome dynamics and symbiosis with microorganisms are briefly discussed.

Indirect selection of implicit mutation protocols

A hypothesis that mutability evolves to facilitate evolutionary adaptation is dismissed by many biologists. Their skepticism is based on a theoretical expectation that natural selection must minimize mutation rates. That view, in turn, is historically grounded in an intuitive presumption that "the vast majority of mutations are harmful." But such skepticism is surely misplaced. Several highly mutagenic genomic patterns, including simple sequence repeats, and transposable elements, are integrated into an unexpectedly large proportion of functional genetic loci. Because alleles arising within such patterns can retain an intrinsic propensity toward a particular style of mutation, natural selection that favors any such allele can indirectly favor the site's mutability as well. By exploiting patterns that have produced beneficial alleles in the past, indirect selection can encourage mutation within constraints that reduce the probability of deleterious effect, thereby shaping implicit "mutation protocols" that effectively promote evolvability.

Evolution of simple sequence repeats as mutable sites

Because natural selection is commonly presumed to minimize mutation rates, the discovery of mutationally unstable simple sequence repeats (SSRs) in many functional genomic locations came as a surprise to many biologists. Whether such SSRs persist in spite of or because of their intrinsic mutability-whether they constitute a genetic burden or an evolutionary boon--remains uncertain. Two contrasting evolutionary explanations can be offered for SSR abundance. First, suppressing the inherent mutability of repetitive sequences might simply lie beyond the reach of natural selection. Alternatively, natural selection might indirectly favor SSRs at sites where particular repeat-number variants have provided positive contributions to fitness. Indirect selection could thereby shape SSRs into "tuning knobs" that facilitate evolutionary adaptation by implementing an implicit protocol of incremental adjustability. The latter possibility is consistent with deep evolutionary conservation of some SSRs, including several in genes with neurological and neurodevelopmental function.