Journal of Evolutionary Biology最新文献

Contact zones between genetically divergent lineages offer a unique opportunity to explore gene flow and speciation dynamics. Because satellite DNAs (satDNAs) have high evolutionary rates, they may be useful for comparing related taxa and assessing contact zones. Here, we analyzed the distribution of chromosomal clusters of PcP190 satDNA across a contact zone between two distinct genetic lineages of a Neotropical species complex of frogs. The parental lineages, Physalaemus ephippifer and lineage 1B (L1B), exhibited pronounced divergence in the number of PcP190 clusters. We further expanded the geographic scope of this species complex by including two additional Brazilian localities in previously available cytogenetic and mitochondrial DNA datasets. The contact zone exhibited remarkable variation in the chromosomal distribution of PcP190 clusters among the autosomes; the only fixed autosomal site was found on chromosome 3. The highest numbers of PcP190 clusters were observed in specimens collected at sites near (approximately 320 km from) the distribution of L1B, whereas specimens from Dom Eliseu, which is near (approximately 330 km from) the distribution of P. ephippifer, had the lowest numbers of such clusters. Mitochondrial haplotypes also exhibited geographical variation across sites. Our findings expand the known contact zone of these Physalaemus lineages from 1,500 km2 to over 6,200 km2, demonstrating its extensive area, and emphasize the usefulness of satDNAs in studying contact zones.

Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundreds or thousands of alignments. Both general models and clade-specific models have been estimated and widely used in phylogenetic analyses. The maximum likelihood method is normally used to select the best fit model for a specific protein alignment under the study. A number of studies have discussed theoretical concerns as well as computational burden of the maximum likelihood methods in model selection. Recently, machine learning methods have been proposed for selecting nucleotide models. In this paper, we propose a method to measure substitution rates among amino acids (called summary statistics) from protein alignments to efficiently train a deep learning network of so-called ModelDetector for detecting amino acid substitution models. The ModelDetector network was trained from 2,246,400 alignments on a computer with 8 cores (without GPU) in about 3.3 hours. Experiments on simulation data showed that the accuracy of the ModelDetector was comparable with that of the maximum likelihood method ModelFinder. It was orders of magnitude faster than the maximum likelihood method in inferring amino acid substitution models and able to analyze genome alignments with millions of sites in minutes. The results indicate that the deep learning network can play as a promising tool for amino acid substitution model selection.

Communication via evolved signals is ubiquitous (both within and between species) in the natural world. However, how honest we should expect signals to be remains an open question. Hybrid equilibria are a form of equilibria predicted by discrete signaling games in which signalers are sometimes dishonest and signals do not completely reliably convey information on signaler quality. While these equilibria have been theoretically demonstrated in several signaling games, their dynamics in a stochastic simulation of evolutionary trajectories (that include representation of the inherent noise expected in evolution in the natural world) have not previously been studied. In this paper, we present an agent-based simulation of a discrete signaling game which exhibits hybrid equilibria. We find that while hybrid equilibria are evolutionarily attractive where they exist, populations exhibit variable and often drastic oscillating behavior around the predicted equilibrium values. We discuss how these dynamics might offer valuable opportunity for detecting hybrid equilibria in natural populations.

There is overwhelming evidence that the microbiome can be important to host physiology and fitness. As such, there is interest in and some theoretical work on understanding when hosts and microbiomes (co)evolve so that microbes benefit hosts and hosts favour beneficial microbes. However, the outcome of evolution likely depends on how microbes benefit hosts. Here, we use adaptive dynamics to investigate how host and symbiont evolution depend on whether symbionts increase host lifespan or host reproduction in a simple model of host and symbiont dynamics. In addition, we investigate 2 ways hosts release (and transmit) symbionts: by releasing symbionts steadily during their lifetime or by releasing them at reproduction, potentially increasing symbionts' chances of infecting the host's offspring. The former is strict horizontal transmission, whereas the latter is also a form of indirect or "pseudovertical" transmission. Our first key result is that the evolution of symbionts that benefit host fecundity requires pseudovertical transmission, while the evolution of symbionts that benefit host lifespan does not. Furthermore, our second key result is that when investing in host benefits is costly to the free-living symbiont stage, intermediate levels of pseudovertical transmission are needed for selection to favour beneficial symbionts. This is true regardless of fitness effects because release at reproduction increases the free-living symbiont population, which increases competition for hosts. Consequently, hosts could evolve away from traits that favour beneficial symbionts. Generally, our work emphasizes the importance of different forms of vertical transmission and fitness benefits in host, microbiome, and holobiont evolution as highlighted by our prediction that the evolution of fecundity-increasing symbionts requires parent-to-offspring transmission.

The mate choice behaviours of females can greatly affect patterns of reproductive success in males and influence the evolution of sexually selected male traits. Population-level estimates of display preferences may provide an accurate estimate of the strength and direction of selection by female choice if all females in the population show homogeneous preferences. However, population-level estimates may yield misleading estimates if there is within-population variation in mate preferences. While it is increasingly clear that the latter situation is common in nature, empirical data on the magnitude of variation in female preferences are required to improve our current understanding of its potential evolutionary consequences. We explored variations in female preference functions for 3 male call properties in a treefrog. We document substantial within-population variation not only in peak preferences but also in preference function shape (open, closed, flat), with at best 62% of females sharing a preference function shape with the respective population curve. Our findings suggest that population curves may accurately capture the direction of sexual selection, but depending on the properties of the constituting individual functions they may over- or underestimate the strength of selection. Particularly population estimates suggesting weak selection may in fact hide the presence of individual females with strong but opposing preferences. Moreover, due to the high within-population variation in both peak preferences and preference function shapes, the population functions drastically underestimate the predicted variation in male mating success in the population.

Eukaryotic energy production requires tight coordination between nuclear and mitochondrial gene products. Because males and females often have different energetic strategies, optimal mitonuclear coordination may be sex-specific. Previous work found evidence for sex-specific mitonuclear effects in the copepod Tigriopus californicus by comparing two parental lines and their reciprocal F1 crosses. However, an alternative hypothesis is that the patterns were driven by the parental source of nuclear alleles. Here, we test this alternative hypothesis by extending the same cross to F2 hybrids, which receive both maternal and paternal nuclear alleles from F1 hybrids. Results confirm mitonuclear effects on sex ratio, with distorted ratios persisting from the F1 to F2 generations, despite reduced fitness in F2 hybrids. No sex-by-cross interactions were found for other phenotypic traits measured. Mitochondrial DNA content was higher in females. Both routine metabolic rate and oxidative DNA damage were lower in F2 hybrids than in parentals. The persistence of sex-specific mitonuclear effects, even in the face of F2 hybrid breakdown, attests to the magnitude of these effects, which contribute to the maintenance of within-population mitochondrial DNA polymorphisms.

Dietary change can be a strong evolutionary force and lead to rapid adaptation in organisms. High-fat and high-sugar diets can challenge key metabolic pathways, negatively affecting other life history traits and inducing pathologies such as obesity and diabetes. In this study, we use experimental evolution to investigate the plastic and evolutionary responses to nutritionally unbalanced diets. We reared replicated lines of larvae of the housefly Musca domestica on a fat-enriched (FAT), a sugar-enriched (SUG), and a control (CTRL) diet for thirteen generations. We measured development time in each generation and larval growth and fat accumulation in generations 1, 7, and 13. Subsequently, all lines were reared for one generation on the control diet to detect any plastic and evolutionary changes. In the first generation, time to pupation decreased on a fat-rich diet and increased on a sugar-rich diet. The fat-rich diet increased fat accumulation and, to a lesser extent, the dry weight of the larvae. Multigenerational exposure to unbalanced diets caused compensatory changes in development time, dry weight, and absolute and relative fat content, although pattern and timing depended on diet and trait. When put back on a control diet, many of the changes induced by the unbalanced diets disappeared, indicating that the diet has large plastic effects. Nevertheless, fat-evolved lines still grew significantly larger than the sugar-evolved lines, and sugar-evolved lines had consistently lower fat content. This can be an effect of parental diet or an evolutionary change in nutrient metabolism as a consequence of multigenerational exposure to unbalanced diets.

The evolution of sexual ornaments in animals is typically attributed to reproductive competition. However, sexual ornaments also arise in contexts where the ornamented sex is neither mate nor gamete limited, and explanations for ornamentation in these cases remain incomplete. In many species, particularly those with slow life histories, lifetime reproductive success depends more strongly on adult survival than fecundity, and survival can depend on intersexual interactions. We develop a population genetic model to investigate how the effect of intersexual interactions on survival may contribute to ornament evolution in the absence of competition for mates. Using female ornamentation in polygynous mating systems as a case study, we show that, indeed, ornaments can evolve when the ornament functions to modify interactions with males in ways that enhance a female's own survival. The evolutionary dynamics depend qualitatively on the specific behavioral mechanism by which the ornament modifies social interactions. In all cases, the ornament's long-term persistence is ultimately determined by the coevolution of the male locus that determines how males affect female survival. We outline the scenarios that are most likely to favor the evolution of female ornaments through the effects of intersexual interactions on survival, and we urge empirical researchers to consider the potential for this social selection mechanism to shape traits of interest across taxa.

Individual vital rates, such as mortality and birth rates, are key determinants of lifetime reproductive success, and variability in these rates shapes population dynamics. Previous studies have found that this vital rate heterogeneity can influence demographic properties, including population growth rates. However, the explicit effects of the variation within and the covariance between vital rates that can also vary throughout the lifespan on population growth remain unknown. Here, we explore the analytical consequences of nongenetic heterogeneity on long-term population growth rates and rates of evolution by modifying traditional age-structured population projection matrices to incorporate variation among individual vital rates. The model allows vital rates to be permanent throughout life ("fixed condition") or to change over the lifespan ("dynamic condition"). We reduce the complexity associated with adding individual heterogeneity to age-structured models through a novel application of matrix collapsing ("phenotypic collapsing"), showing how to collapse in a manner that preserves the asymptotic and transient dynamics of the original matrix. The main conclusion is that nongenetic individual heterogeneity can strongly impact the long-term growth rate and rates of evolution. The magnitude and sign of this impact depend heavily on how the heterogeneity covaries across the lifespan of an organism. Our results emphasize that nongenetic variation cannot simply be viewed as random noise, but rather that it has consistent, predictable effects on fitness and evolvability.

Differential migration strategies favour different sets of characteristics, including sexually selected ornamentation. Such phenotypic variation is particularly evident in a population with partial migration, where migrants and nonmigrants co-exist. Partial migration provides insights into the link among migration, local environment, and ornamentation, although empirical studies remain scarce. Here, we studied the plumage traits of barn swallows (Hirundo rustica) in southern Japan, where both winterings and migrants breed sympatrically. We further examined this relationship with multiple isotopes (δ2H, δ13C, δ15N, and δ34S), which provides insight into their moulting habitat. Among males, winterings and migrants differed in their morphological traits: wintering males had shorter wings, which suggests the high demand for flight apparatus in migratory birds. Moreover, wintering males had larger white tail spots and less colourful throat patches than migratory males, indicating ornament divergence between them. Wintering males had a significantly smaller isotopic space when examining the combinations of δ34S with the other isotopes compared to migratory males, which indicates a differential geographic range between them, perhaps because of the limited variation in the distance to the sea in wintering males. As in males, wintering females had a significantly smaller isotopic space than migrant females, but there were few morphological differences between migratory and wintering females. Instead, some morphological traits were related to isotope values in females. These results indicate sex-specific linkage among migration, local environment, and ornamentation.