Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids.

Hybridization and polyploidy are powerful evolutionary forces, inducing a range of phenotypic outcomes, including non-additive expression, subgenome dominance, deviations in genomic dosage, and transcriptome downsizing. The reasons for these patterns and whether they are universal adaptive responses to genome merging and doubling remain debated. To address this, we develop a thermodynamic model of gene expression based on transcription factor (TF)-promoter binding. Applied to hybridization between species with divergent gene expression levels, cell volumes, or euchromatic ratios, this model distinguishes the effects of hybridization from those of polyploidy. Our results align with empirical observations, suggesting that gene regulation patterns in hybrids and polyploids often stem from the constrained interplay between inherited diverged regulatory networks rather than from subsequent adaptive evolution. In addition, occurrence of certain phenotypic traits depend on specific assumptions about promoter-TF coevolution and their distribution within the hybrid's nucleoplasm, offering new research avenues to understand the underlying mechanisms. In summary, our model explains how the legacy of divergent species directly influences the phenotypic traits of hybrids and allopolyploids.

Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function.

Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.

Sperm-dependent asexual hybrids determine competition among sexual species.

Interspecific competition is a fundamental process affecting community structure and evolution of interacting species. Besides direct competition, this process is also mediated by shared enemies, which can change the outcome of competition dramatically. However, previous studies investigating interactions between competing species and their parasites (parasite-mediated competition) completely overlooked the effect of 'sperm' parasites (i.e. sperm-dependent parthenogens or pseudogams) on competition. These organisms originate by interspecific hybridization, produce clonal gametes, but exploit parental species for their own reproduction, being therefore analogous to classical parasites. Here we use the reaction-diffusion model and show that pseudogams alter the outcome of interspecific competition significantly. They may either slow down competitive exclusion of the inferior competitor or even turn the outcome of competition between the species. Asexual organisms may thus have unexpectedly strong impact on community structure, and have more significant evolutionary potential than was previously thought.

Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models.

BACKGROUND: Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet). However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200.) reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them. RESULTS AND DISCUSSION: We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality. CONCLUSIONS: Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the possibility that processes affecting clonal evolution differ from those described in recent studies, suggesting that theoretical models of asexual populations must evolve to address this problem in detail. REVIEWERS: This article was reviewed by Isa Schön (nominated by John Logsdon), Arcady Mushegian and Timothy G. Barraclough (nominated by Laurence Hurst).

Adaptive foraging does not always lead to more complex food webs.

Recent modeling studies exploring the effect of consumers' adaptivity in diet composition on food web complexity invariably suggest that adaptivity in foraging decisions of consumers makes food webs more complex. That is, it allows for survival of a higher number of species when compared with non-adaptive food webs. Population-dynamical models in these studies share two features: parameters are chosen uniformly for all species, i.e. they are species-independent, and adaptive foraging is described by the search image model. In this article, we relax both these assumptions. Specifically, we allow parameters to vary among the species and consider the diet choice model as an alternative model of adaptive foraging. Our analysis leads to three important predictions. First, for species-independent parameter values for which the search image model demonstrates a significant effect of adaptive foraging on food web complexity, the diet choice model produces no such effect. Second, the effect of adaptive foraging through the search image model attenuates when parameter values cease to be species-independent. Finally, for the diet choice model we observe no (significant) effect of adaptive foraging on food web complexity. All these observations suggest that adaptive foraging does not always lead to more complex food webs. As a corollary, future studies of food web dynamics should pay careful attention to the choice of type of adaptive foraging model as well as of parameter values.

The effect of the Holling type II functional response on apparent competition.

This article analyzes the classical 2-resource-1-consumer apparent competition community module with the Holling type II functional response. Two types of resource regulation (top-down vs. combined top-down and bottom-up) and two types of consumer behaviors (inflexible consumers with fixed preferences for resources vs. adaptive consumers) are considered. When resources grow exponentially and consumers are inflexible foragers, one resource is always outcompeted due to strong apparent competition. Density dependent resource growth relaxes apparent competition so that resources can coexist. As multiple attractors (either equilibria or limit cycles) coexist, population dynamics and community composition depend on initial population densities. Population dynamics change dramatically when consumers forage adaptively. In this case, the results both for top-down, and combined top-down and bottom-up regulation are similar and they show that species persistence occurs for a much larger set of parameter values when compared with inflexible consumers. Moreover, population dynamics will be chaotic when resource carrying capacities are high enough. This shows that adaptive consumer switching can destabilize population dynamics.

Optimal foraging and predator-prey dynamics III.

In the previous two articles (Theor. Popul. Biol. 49 (1996) 265-290; 55 (1999) 111-126), the population dynamics resulting from a two-prey-one-predator system with adaptive predators was studied. In these articles, predators followed the predictions of optimal foraging theory. Analysis of that system was hindered by the incorporation of the logistic description of prey growth. In particular, because prey self-regulation dependence is a strong stabilizing mechanism, the effects of optimal foraging could not be easily separated from the effects of bottom-up control of prey growth on species coexistence. In this article, we analyze two models. The first model assumes the exponential growth of both prey types while the second model assumes the exponential growth of the preferred prey type and the logistic growth of the alternative prey type. This permits the effect of adaptive foraging on two-prey-predator food webs to be addressed. We show that optimal foraging reduces apparent competition between the two prey types, promotes species coexistence, and leads to multiple attractors.