Evolutionary Causes Research Articles

Distribution of human single-nucleotide polymorphisms is approximated by the power law and represents a fractal structure.

Single-nucleotide polymorphisms (SNPs) are one of the main causes of evolution. The distribution of human SNPs, which were examined in detail genomewide, was analyzed. Three discrete databases of human SNPs were used for this analysis, and similar results were obtained from these databases. It was found that the distribution of the distance between SNPs was approximated by the power law, and the shape of the regions including SNPs had the so-called fractal structure. Although the reason why the distribution of SNPs obeys such a certain law of physics is unclear, a speculation was attempted in connection with the three-dimensional structure of human chromatin which has a fractal structure.

Selection and constraints on offspring size-number trade-offs in sand lizards (Lacerta agilis).

The trade-off between offspring size and number is a central component of life-history theory, postulating that larger investment into offspring size inevitably decreases offspring number. This trade-off is generally discussed in terms of genetic, physiological or morphological constraints; however, as among-individual differences can mask individual trade-offs, the underlying mechanisms may be difficult to reveal. In this study, we use multivariate analyses to investigate whether there is a trade-off between offspring size and number in a population of sand lizards by separating among- and within-individual patterns using a 15-year data set collected in the wild. We also explore the ecological and evolutionary causes and consequences of this trade-off by investigating how a female's resource (condition)- vs. age-related size (snout-vent length) influences her investment into offspring size vs. number (OSN), whether these traits are heritable and under selection and whether the OSN trade-off has a genetic component. We found a negative correlation between offspring size and number within individual females and physical constraints (size of body cavity) appear to limit the number of eggs that a female can produce. This suggests that the OSN trade-off occurs due to resource constraints as a female continues to grow throughout life and, thus, produces larger clutches. In contrast to the assumptions of classic OSN theory, we did not detect selection on offspring size; however, there was directional selection for larger clutch sizes. The repeatabilities of both offspring size and number were low and we did not detect any additive genetic variance in either trait. This could be due to strong selection (past or current) on these life-history traits, or to insufficient statistical power to detect significant additive genetic effects. Overall, the findings of this study are an important illustration of how analyses of within-individual patterns can reveal trade-offs and their underlying causes, with potential evolutionary and ecological consequences that are otherwise hidden by among-individual variation.

Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation.

Modern enzymes are highly optimized biocatalysts that process their substrates with extreme efficiency. Many enzymes catalyze more than one reaction; however, the persistence of such ambiguities, their consequences and evolutionary causes are largely unknown. As a paradigmatic case, we study the history of bi-functionality for a time span of approximately two billion years for the sugar isomerase HisA from histidine biosynthesis. To look back in time, we computationally reconstructed and experimentally characterized three HisA predecessors. We show that these ancient enzymes catalyze not only the HisA reaction but also the isomerization of a similar substrate, which is commonly processed by the isomerase TrpF in tryptophan biosynthesis. Moreover, we found that three modern-day HisA enzymes from Proteobacteria and Thermotogae also possess low TrpF activity. We conclude that this bi-functionality was conserved for at least two billion years, most likely without any evolutionary pressure. Although not actively selected for, this trait can become advantageous in the case of a gene loss. Such exaptation is exemplified by the Actinobacteria that have lost the trpF gene but possess the bi-functional HisA homolog PriA, which adopts the roles of both HisA and TrpF. Our findings demonstrate that bi-functionality can perpetuate in the absence of selection for very long time-spans.

Phylogeny of Aging and Related Phenoptotic Phenomena.

The interpretation of aging as adaptive, i.e. as a phenomenon genetically determined and modulated, and with an evolutionary advantage, implies that aging, as any physiologic mechanism, must have phylogenetic connections with similar phenomena. This review tries to find the phylogenetic connections between vertebrate aging and some related phenomena in other species, especially within those phenomena defined as phenoptotic, i.e. involving the death of one or more individuals for the benefit of other individuals. In particular, the aim of the work is to highlight and analyze similarities and connections, in the mechanisms and in the evolutionary causes, between: (i) proapoptosis in prokaryotes and apoptosis in unicellular eukaryotes; (ii) apoptosis in unicellular and multicellular eukaryotes; (iii) aging in yeast and in vertebrates; and (iv) the critical importance of the DNA subtelomeric segment in unicellular and multicellular eukaryotes. In short, there is strong evidence that vertebrate aging has clear similarities and connections with phenomena present in organisms with simpler organization. These phylogenetic connections are a necessary element for the sustainability of the thesis of aging explained as an adaptive phenomenon, and, on the contrary, are incompatible with the opposite view of aging as being due to the accumulation of random damages of various kinds.

Subspecific variation in sperm morphology and performance in the Long-tailed Finch (Poephila acuticauda)

Evolutionary biology endeavours to explain biological diversity, and as such it is critical to develop an understanding of the adaptive and functional significance of trait variation. Spermatozoa exhibit remarkable levels of morphological diversification. However, our understanding of the evolutionary causes and functional significance of this variation is limited, especially at the intraspecific level. We quantified variation in sperm morphology and performance between two subspecies of Long-tailed Finch (Poephila acuticauda acuticauda and P. a. hecki), a small grassfinch found in tropical northern Australia. Despite a zone of secondary contact, these subspecies are maintained as two distinct forms: P. a. acuticauda occurs in the western part of the species’ range and has a yellow bill, while P. a. hecki exhibits a red bill and is found in the eastern part of the range. We found small, but significant differences in sperm size between these subspecies (P. a. acuticauda had longer and narrower sperm than P. a. hecki), which was surprising given the recent evolutionary origins of these two taxa (i.e. 0.3 million years ago). Additionally, both subspecies exhibited high values of between- and within-male variation in sperm morphology, though in the case of sperm midpiece length this variation was significantly lower in P. a. acuticauda relative to P. a. hecki. We suggest these observed differences in sperm morphology are the result of genetic drift and reflect historical processes associated with divergence between the eastern and western populations of these two subspecies. Finally, we discuss the potential implications of our findings for the process of population divergence and reproductive isolation.

Population density of the Réunion Grey White-eye Zosterops borbonicus within the summit ecosystems of Réunion, Mascarene Islands

Assessing population density is crucial for studying the ecology and evolutionary biology of species as well as for conservation purposes. Here we used point count methods to infer population density in a single-island endemic passerine bird, the Réunion Grey White-eye Zosterops borbonicus, that displays striking evidence of differentiation at a small spatial scale. Population density was estimated at 5.17 birds ha−1 (CL 4.85–5.50), a value somewhat higher than previously believed. This estimation provides the first detailed estimation of bird population density in the vulnerable summit ecosystems of Réunion and will possibly allow a better understanding of the evolutionary causes of this plumage colour variation.

The Causal Structure of Evolutionary Theory

ABSTRACTOne contentious debate in the philosophy of biology is that between the statisticalists and causalists. The former understand core evolutionary concepts like fitness and selection to be mere statistical summaries of underlying causal processes. In this view, evolutionary changes cannot be causally explained by selection or fitness. The causalist side, on the other hand, holds that populations can change in response to selection—one can cite fitness differences or driftability in causal explanations of evolutionary change. But, on the causalist side, it is often not clear how, precisely, one should understand these causes. Thus, much more could be said about what sort of causes fitness and driftability are. In this paper, I borrow Dretske's distinction between structuring and triggering causes and I suggest that fitness and driftability are structuring causes of evolution.

A complex mode of aggressive mimicry in a scale-eating cichlid fish.

Aggressive mimicry is an adaptive tactic of parasitic or predatory species that closely resemble inoffensive models in order to increase fitness via predatory gains. Although similarity of distantly related species is often intuitively implicated with mimicry, the exact mechanisms and evolutionary causes remain elusive in many cases. Here, we report a complex aggressive mimicry strategy in Plecodus straeleni, a scale-eating cichlid fish from Lake Tanganyika, which imitates two other cichlid species. Employing targeted sequencing on ingested scales, we show that P. straeleni does not preferentially parasitize its models but—contrary to prevailing assumptions—targets a variety of co-occurring dissimilar looking fish species. Combined with tests for visual resemblance and visual modelling from a prey perspective, our results suggest that complex interactions among different cichlid species are involved in this mimicry system.

Symbiotic interactions in the Ordovician of Baltica

Eleven symbiotic associations between taxa occur in the Ordovician of Baltica, most involving colonial animals. Bryozoans formed the most numerous associations (including possible polychaete bioclaustrations, possible polychaete borings, conulariids, and crinoids) and had the highest number of symbiosis cases. In Baltica, the Late Ordovician symbiotic associations differ from those in the Middle Ordovician by a remarkable increase in the numbers of recorded cases. This is most likely explained by the Great Ordovician Biodiversification Event (GOBE). The higher faunal diversity may have created more opportunities for symbiotic relationships. These changes in the symbiotic interactions in the Ordovician of Baltica were probably not related to climate change, but had an evolutionary cause.

Rapid and widespread de novo evolution of kin discrimination

Diverse forms of kin discrimination, broadly defined as alteration of social behavior as a function of genetic relatedness among interactants, are common among social organisms from microbes to humans. However, the evolutionary origins and causes of kin-discriminatory behavior remain largely obscure. One form of kin discrimination observed in microbes is the failure of genetically distinct colonies to merge freely upon encounter. Here, we first use natural isolates of the highly social bacterium Myxococcus xanthus to show that colony-merger incompatibilities can be strong barriers to social interaction, particularly by reducing chimerism in multicellular fruiting bodies that develop near colony-territory borders. We then use experimental laboratory populations to test hypotheses regarding the evolutionary origins of kin discrimination. We show that the generic process of adaptation, irrespective of selective environment, is sufficient to repeatedly generate kin-discriminatory behaviors between evolved populations and their common ancestor. Further, we find that kin discrimination pervasively evolves indirectly between allopatric replicate populations that adapt to the same ecological habitat and that this occurs generically in many distinct habitats. Patterns of interpopulation discrimination imply that kin discrimination phenotypes evolved via many diverse genetic mechanisms and mutation-accumulation patterns support this inference. Strong incompatibility phenotypes emerged abruptly in some populations but strengthened gradually in others. The indirect evolution of kin discrimination in an asexual microbe is analogous to the indirect evolution of reproductive incompatibility in sexual eukaryotes and linguistic incompatibility among human cultures, the commonality being indirect, noncoordinated divergence of complex systems evolving in isolation.

When is dispersal for dispersal? Unifying marine and terrestrial perspectives.

Recent syntheses on the evolutionary causes of dispersal have focused on dispersal as a direct adaptation, but many traits that influence dispersal have other functions, raising the question: when is dispersal 'for' dispersal? We review and critically evaluate the ecological causes of selection on traits that give rise to dispersal in marine and terrestrial organisms. In the sea, passive dispersal is relatively easy and specific morphological, behavioural, and physiological adaptations for dispersal are rare. Instead, there may often be selection to limit dispersal. On land, dispersal is relatively difficult without specific adaptations, which are relatively common. Although selection for dispersal is expected in both systems and traits leading to dispersal are often linked to fitness, systems may differ in the extent to which dispersal in nature arises from direct selection for dispersal or as a by-product of selection on traits with other functions. Our analysis highlights incompleteness of theories that assume a simple and direct relationship between dispersal and fitness, not just insofar as they ignore a vast array of taxa in the marine realm, but also because they may be missing critically important effects of traits influencing dispersal in all realms.

A test of genetic models for the evolutionary maintenance of same-sex sexual behaviour.

The evolutionary maintenance of same-sex sexual behaviour (SSB) has received increasing attention because it is perceived to be an evolutionary paradox. The genetic basis of SSB is almost wholly unknown in non-human animals, though this is key to understanding its persistence. Recent theoretical work has yielded broadly applicable predictions centred on two genetic models for SSB: overdominance and sexual antagonism. Using Drosophila melanogaster, we assayed natural genetic variation for male SSB and empirically tested predictions about the mode of inheritance and fitness consequences of alleles influencing its expression. We screened 50 inbred lines derived from a wild population for male-male courtship and copulation behaviour, and examined crosses between the lines for evidence of overdominance and antagonistic fecundity selection. Consistent variation among lines revealed heritable genetic variation for SSB, but the nature of the genetic variation was complex. Phenotypic and fitness variation was consistent with expectations under overdominance, although predictions of the sexual antagonism model were also supported. We found an unexpected and strong paternal effect on the expression of SSB, suggesting possible Y-linkage of the trait. Our results inform evolutionary genetic mechanisms that might maintain low but persistently observed levels of male SSB in D. melanogaster, but highlight a need for broader taxonomic representation in studies of its evolutionary causes.

Social carry-over effects on non-social behavioral variation: mechanisms and consequences

The field of animal personality is interested in decomposing behaviors into different levels of variation, with its present focus on the ecological and evolutionary causes and consequences of expressed variation. Recently the role of the social environment, i.e. social partners, has been suggested to affect behavioral variation and induce selection on animal personality. Social partner effects exist because characters of social partners (e.g. size, behavior), affect the behavioral expression of a focal individual. Here, we 1) first review the proximate mechanisms underlying the social partner effects on behavioral expression and the timescales at which such effects might take place. We then 2) discuss how within- and among-individual variation in single behaviors and covariation between multiple behaviors, caused by social partners, can carry-over to non-social behaviors expressed outside the social context. Finally, we 3) highlight evolutionary consequences of social carry-over effects to non-social behaviors and 4) suggest study designs and statistical approaches which can be applied to study the nature and evolutionary consequences of social carry-over effects on non-social behaviors. Understanding the proximate mechanisms underpinning the social partner effects is important since it opens a door for deeper understanding of how social environments can affect behavioral variation and covariation at multiple levels, and the evolution of non-social behaviors (i.e. exploration, activity, boldness) that are affected by social interactions.

Early Stress Causes Sex-Specific, Life-Long Changes in Behaviour, Levels of Gonadal Hormones, and Gene Expression in Chickens

Early stress can have long-lasting phenotypic effects. Previous research shows that male and female chickens differ in many behavioural aspects, and respond differently to chronic stress. The present experiment aimed to broadly characterize long-term sex differences in responses to brief events of stress experienced during the first weeks of life. Chicks from a commercial egg-laying hybrid were exposed to stress by inducing periods of social isolation during their first three weeks of life, followed by a broad behavioural, physiological and genomic characterization throughout life. Early stressed males, but not females, where more anxious in an open field-test, stayed shorter in tonic immobility and tended to have delayed sexual maturity, as shown by a tendency for lower levels of testosterone compared to controls. While early stressed females did not differ from non-stressed in fear and sexual maturation, they were more socially dominant than controls. The differential gene expression profile in hypothalamus was significantly correlated from 28 to 213 days of age in males, but not in females. In conclusion, early stress had a more pronounced long-term effect on male than on female chickens, as evidenced by behavioral, endocrine and genomic responses. This may either be attributed to inherent sex differences due to evolutionary causes, or possibly to different stress related selection pressures on the two sexes during commercial chicken breeding.

Extreme recombination frequencies shape genome variation and evolution in the honeybee, Apis mellifera.

Meiotic recombination is a fundamental cellular process, with important consequences for evolution and genome integrity. However, we know little about how recombination rates vary across the genomes of most species and the molecular and evolutionary determinants of this variation. The honeybee, Apis mellifera, has extremely high rates of meiotic recombination, although the evolutionary causes and consequences of this are unclear. Here we use patterns of linkage disequilibrium in whole genome resequencing data from 30 diploid honeybees to construct a fine-scale map of rates of crossing over in the genome. We find that, in contrast to vertebrate genomes, the recombination landscape is not strongly punctate. Crossover rates strongly correlate with levels of genetic variation, but not divergence, which indicates a pervasive impact of selection on the genome. Germ-line methylated genes have reduced crossover rate, which could indicate a role of methylation in suppressing recombination. Controlling for the effects of methylation, we do not infer a strong association between gene expression patterns and recombination. The site frequency spectrum is strongly skewed from neutral expectations in honeybees: rare variants are dominated by AT-biased mutations, whereas GC-biased mutations are found at higher frequencies, indicative of a major influence of GC-biased gene conversion (gBGC), which we infer to generate an allele fixation bias 5 – 50 times the genomic average estimated in humans. We uncover further evidence that this repair bias specifically affects transitions and favours fixation of CpG sites. Recombination, via gBGC, therefore appears to have profound consequences on genome evolution in honeybees and interferes with the process of natural selection. These findings have important implications for our understanding of the forces driving molecular evolution.

Squamate hatchling size and the evolutionary causes of negative offspring size allometry

Although fecundity selection is ubiquitous, in an overwhelming majority of animal lineages, small species produce smaller number of offspring per clutch. In this context, egg, hatchling and neonate sizes are absolutely larger, but smaller relative to adult body size in larger species. The evolutionary causes of this widespread phenomenon are not fully explored. The negative offspring size allometry can result from processes limiting maximal egg/offspring size forcing larger species to produce relatively smaller offspring ('upper limit'), or from a limit on minimal egg/offspring size forcing smaller species to produce relatively larger offspring ('lower limit'). Several reptile lineages have invariant clutch sizes, where females always lay either one or two eggs per clutch. These lineages offer an interesting perspective on the general evolutionary forces driving negative offspring size allometry, because an important selective factor, fecundity selection in a single clutch, is eliminated here. Under the upper limit hypotheses, large offspring should be selected against in lineages with invariant clutch sizes as well, and these lineages should therefore exhibit the same, or shallower, offspring size allometry as lineages with variable clutch size. On the other hand, the lower limit hypotheses would allow lineages with invariant clutch sizes to have steeper offspring size allometries. Using an extensive data set on the hatchling and female sizes of >1800 species of squamates, we document that negative offspring size allometry is widespread in lizards and snakes with variable clutch sizes and that some lineages with invariant clutch sizes have unusually steep offspring size allometries. These findings suggest that the negative offspring size allometry is driven by a constraint on minimal offspring size, which scales with a negative allometry.

Acceptance threshold theory can explain occurrence of homosexual behaviour.

Same-sex sexual behaviour (SSB) has been documented in a wide range of animals, but its evolutionary causes are not well understood. Here, we investigated SSB in the light of Reeve's acceptance threshold theory. When recognition is not error-proof, the acceptance threshold used by males to recognize potential mating partners should be flexibly adjusted to maximize the fitness pay-off between the costs of erroneously accepting males and the benefits of accepting females. By manipulating male burying beetles' search time for females and their reproductive potential, we influenced their perceived costs of making an acceptance or rejection error. As predicted, when the costs of rejecting females increased, males exhibited more permissive discrimination decisions and showed high levels of SSB; when the costs of accepting males increased, males were more restrictive and showed low levels of SSB. Our results support the idea that in animal species, in which the recognition cues of females and males overlap to a certain degree, SSB is a consequence of an adaptive discrimination strategy to avoid the costs of making rejection errors.

Variation in pollen limitation and floral parasitism across a mating system transition in a Pacific coastal dune plant: evolutionary causes or ecological consequences?

Evolutionary transitions from outcrossing to self-fertilization are thought to occur because selfing provides reproductive assurance when pollinators or mates are scarce, but they could also occur via selection to reduce floral vulnerability to herbivores. This study investigated geographic covariation between floral morphology, fruit set, pollen limitation and florivory across the geographic range of Camissoniopsis cheiranthifolia, a Pacific coastal dune endemic that varies strikingly in flower size and mating system. Fruit set was quantified in 75 populations, and in 41 of these floral herbivory by larvae of a specialized moth (Mompha sp.) that consumes anthers in developing buds was also quantified. Experimental pollen supplementation was performed to quantify pollen limitation in three large-flowered, outcrossing and two small-flowered, selfing populations. These parameters were also compared between large- and small-flowered phenotypes within three mixed populations. Fruit set was much lower in large-flowered populations, and also much lower among large- than small-flowered plants within populations. Pollen supplementation increased per flower seed production in large-flowered but not small-flowered populations, but fruit set was not pollen limited. Hence inadequate pollination cannot account for the low fruit set of large-flowered plants. Floral herbivory was much more frequent in large-flowered populations and correlated negatively with fruit set. However, florivores did not preferentially attack large-flowered plants in three large-flowered populations or in two of three mixed populations. Selfing alleviated pollen limitation of seeds per fruit, but florivory better explains the marked variation in fruit set. Although florivory was more frequent in large-flowered populations, large-flowered individuals were not generally more vulnerable within populations. Rather than a causative selective factor, reduced florivory in small-flowered, selfing populations is probably an ecological consequence of mating system differentiation, with potentially significant effects on population demography and biotic interactions.

Causal Foundations of Evolutionary Genetics

The causal nature of evolution is one of the central topics in the philosophy of biology. The issue concerns whether equations used in evolutionary genetics point to some causal processes or purely phenomenological patterns. To address this question the present article builds well-defined causal models that underlie standard equations in evolutionary genetics. These models are based on minimal and biologically plausible hypotheses about selection and reproduction, and generate statistics to predict evolutionary changes. The causal reconstruction of the evolutionary principles shows adaptive evolution as a genuine causal process, where fitness and selection are both causes of evolution. 1 Introduction 2 The Philosophical Puzzle 3 Causal Models 4 Causal Foundations of Evolutionary Genetics 4.1 Univariate quantitative genetics model 4.1.1 The causal graph 4.1.2 Structural equations 4.1.3 Deriving evolutionary transition functions 4.2 One-locus population genetics model 5 Evolution as a Causal Process 5.1 Selection as a causal process 5.2 Causes of evolutionary change 6 Conclusion

On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms.

Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.