Implications For Adaptive Evolution Research Articles

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.

Soil burial induced dormancy in weedy rice seeds through hormone level changes: Implications in adaptive evolution and weed control

AbstractSeed dormancy plays a key role in preventing seeds of higher plants from random germination under adverse environmental conditions. Previous studies suggested that a critical temperature could regulate germination of weedy rice seeds without primary dormancy at seed dispersion. However, what will happen to the non‐dormant seeds after shattering in the soil seed banks when temperature fluctuates to exceed the critical temperature remains an interesting question to be investigated. To determine whether or not soil burial can change the status of dormancy in weedy rice seeds, we examined germination ratios of weedy rice seeds after soil‐burial treatments. In addition, we compared hormone levels in the untreated seeds and viable but ungerminated seeds after soil burial. Results showed that soil burial induced a proportion of 41%–72% dormant seeds in the initially non‐dormant weedy rice seeds. Also, the induction of seed dormancy is associated with the change of hormone levels in the seeds treated by soil burial, suggesting that soil burial can significantly activate the control of hormone production in seeds. Together, the previously reported mechanism of critical temperature‐inhibited seed germination and the newly found phenomenon of soil burial‐induced seed dormancy provide a “double‐security” strategy to ensure germination of weedy rice seeds under a favorable condition in agricultural ecosystems. The findings not only reveal the important role of rapid evolution of adaptive functions in weeds, such as weedy rice, in adapting to changing agricultural environments, but also facilitate the design of strategies for effective weedy rice control practices.

Self-fertilization and inbreeding limit the scope for sexually antagonistic polymorphism.

Sexual antagonism occurs when there is a positive intersexual genetic correlation in trait expression but opposite fitness effects of the trait(s) in males and females. As such, it constrains the evolution of sexual dimorphism and may therefore have implications for adaptive evolution. There is currently considerable evidence for the existence of sexually antagonistic genetic variation in laboratory and natural populations, but how sexual antagonism interacts with other evolutionary phenomena is still poorly understood in many cases. Here, we explore how self-fertilization and inbreeding affect the maintenance of polymorphism for sexually antagonistic loci. We expected a priori that selfing should reduce the region of polymorphism, as inbreeding reduces the frequency of heterozygotes and speeds fixation. This expectation was supported, but although previous results suggest that the more an allele that is deleterious to one sex is dominant in that sex, the smaller the region of parameter space that will admit polymorphism, we found that this effect is weakened by self-fertilization. However, the effect of inbreeding is not strong enough to completely cancel out the effect of dominance: For a given frequency of inbreeding, it will still be the case that the more dominant the alleles are in their deleterious context, the smaller the region of parameter space in which they can exist at polymorphism.

Elevational range expansion in a neotropical live-bearing fish from Panama: implications for adaptive evolution

The live-bearing fish genus Brachyrhaphis from Central America has become an important model system in evolutionary and ecological research. This paper presents some of the first work on the Cardinal Olomina Brachyrhaphis roseni since this species was first described. Specifically, I present data on populations that suggest that the elevational distribution of B. roseni is dramatically different than what was previously thought. This work will provide valuable background information for future studies of the ecology and evolution of this species.

The Price Equation and Extended Inheritance

The presence of various mechanisms of non-genetic inheritance is one of the main problems for current evolutionary theory according to several critics. Sufficient empirical and conceptual reasons exist to take this claim seriously, but there is little consensus on the implications of multiple inheritance systems for evolutionary processes. Here we use the Price Equation as a starting point for a discussion of the differences between four recently proposed categories of inheritance systems; genetic, epigenetic, behavioral and symbolic. Specifically, we address how the components of the Price Equation encompass different non-genetic systems of inheritance in an attempt to clarify how the different systems are conceptually related. We conclude that the four classes of inheritance systems do not form distinct clusters with respect to their effect on the rate and direction of phenotypic change from one generation to the next in the absence or presence of selection. Instead, our analyses suggest that different inheritance systems can share features that are conceptually very similar, but that their implications for adaptive evolution nevertheless differ substantially as a result of differences in their ability to couple selection and inheritance.

Duplication and functional diversification of pancreatic ribonuclease (RNASE1) gene

Adaptation is one of the most fundamental issues in the studies of organismal evolution. Pancreatic ribonuclease is a very important digestive enzyme and secreted by the pancreas. Numerous studies have suggested that RNASE1 gene duplication is closely related to the functional adaptation of the digestive system in the intestinal fermentation herbivores. RNASE1 gene thus becomes one of the most important candidate genetic markers to study the molecular mechanism of adaptation of organisms to the feeding habit. Interestingly, RNASE1 gene duplication has also been found in some non-intestinal fermentation mammals, suggesting that RNASE1 gene may have produced novel tissue specificity or functions in these species. In this review, RNASE1 gene and its implications in adaptive evolution, especially in association with the feeding habit of organisms, are summarized.

Do human and JC virus genes show evidence of host–parasite codemography?

Information about similarities and differences in the demographic history of host and parasite populations is potentially useful for making inferences about a variety of evolutionary processes. However, it is difficult to observe the historical demographic properties of natural populations directly. Here, the extent of demographic similarity in a host and its parasite was examined indirectly by inferring long-term population history from patterns of genetic variation. Nucleotide sequence diversity in human and JC virus (JCV) DNA is consistent with a long-term demographic connection between the two species: both show evidence of large-scale population expansion. However, genetic data also suggest that the two species have different patterns of population substructuring. These similarities and differences have implications for adaptive evolution in JCV that are not evident when the two species are considered separately.