Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

Background

Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages when comparing the genetic associations between glass eels and silver eels.

Results

We used two sets of markers to test for selection: first, we genotyped individuals using a panel of 80 coding-gene single nucleotide polymorphisms (SNPs) developed in American eel; second, we investigated selection at the genome level using a total of 153,423 RAD-sequencing generated SNPs widely distributed across the genome. Using the RAD approach, outlier tests identified a total of 2413 (1.57 %) potentially selected SNPs. Functional annotation analysis identified signal transduction pathways as the most over-represented group of genes, including MAPK/Erk signalling, calcium signalling and GnRH (gonadotropin-releasing hormone) signalling. Many of the over-represented pathways were related to growth, while others could result from the different conditions that eels inhabit during their life cycle.

Conclusions

The observation of different genes and gene pathways under selection when comparing glass eels vs. silver eels supports the adaptive decoupling hypothesis for the benefits of metamorphosis. Partitioning the life cycle into discrete morphological phases may be overall beneficial since it allows the different life stages to respond independently to their unique selection pressures. This might translate into a more effective use of food and niche resources and/or performance of phase-specific tasks (e.g. feeding in the case of glass eels, migrating and reproducing in the case of silver eels).

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1754-3) contains supplementary material, which is available to authorized users.     

Evolution of complex life cycles in trophically transmitted helminths. I. Host incorporation and trophic ascent

Links between parasites and food webs are evolutionarily ancient but dynamic: life history theory provides insights into helminth complex life cycle origins. Most adult helminths benefit by sexual reproduction in vertebrates, often high up food chains, but direct infection is commonly constrained by a trophic vacuum between free‐living propagules and definitive hosts. Intermediate hosts fill this vacuum, facilitating transmission to definitive hosts. The central question concerns why sexual reproduction, and sometimes even larval growth, is suppressed in intermediate hosts, favouring growth arrest at larval maturity in intermediate hosts and reproductive suppression until transmission to definitive hosts? Increased longevity and higher growth in definitive hosts can generate selection for larger parasite body size and higher fecundity at sexual maturity. Life cycle length is increased by two evolutionary mechanisms, upward and downward incorporation, allowing simple (one‐host) cycles to become complex (multihost). In downward incorporation, an intermediate host is added below the definitive host: models suggest that downward incorporation probably evolves only after ecological or evolutionary perturbations create a trophic vacuum. In upward incorporation, a new definitive host is added above the original definitive host, which subsequently becomes an intermediate host, again maintained by the trophic vacuum: theory suggests that this is plausible even under constant ecological/evolutionary conditions. The final cycle is similar irrespective of its origin (upward or downward). Insights about host incorporation are best gained by linking comparative phylogenetic analyses (describing evolutionary history) with evolutionary models (examining selective forces). Ascent of host trophic levels and evolution of optimal host taxa ranges are discussed.     

Fast life history traits promote invasion success in amphibians and reptiles

Competing theoretical models make different predictions on which life history strategies facilitate growth of small populations. While ‘fast’ strategies allow for rapid increase in population size and limit vulnerability to stochastic events, ‘slow’ strategies and bet‐hedging may reduce variance in vital rates in response to stochasticity. We test these predictions using biological invasions since founder alien populations start small, compiling the largest dataset yet of global herpetological introductions and life history traits. Using state‐of‐the‐art phylogenetic comparative methods, we show that successful invaders have fast traits, such as large and frequent clutches, at both establishment and spread stages. These results, together with recent findings in mammals and plants, support ‘fast advantage’ models and the importance of high potential population growth rate. Conversely, successful alien birds are bet‐hedgers. We propose that transient population dynamics and differences in longevity and behavioural flexibility can help reconcile apparently contrasting results across terrestrial vertebrate classes.     

Toward bridging the gap between life and physics

Examination of the scale properties of living organisms and the electronic configuration of crystalline structures suggests that related modeling may be used for both. This paper comments on individual and common properties of the two systems and draws a comparison between them. Both exhibit multiple ‘scales’ separated by complex or forbidden regions and a global ‘overview’ of their scale properties. We conclude that the analogy may provide a fruitful route toward extension of the modeling of both living organisms and electronic materials, by permitting bootstrapping cross-modeling between them.     

Models of metamorphic timing: an experimental evaluation with the pond-dwelling salamander Hemidactylium scutatum (Caudata: Plethodontidae)

Amphibian larvae vary tremendously in size at metamorphosis and length of larval period. We raised pond-dwelling four-toed salamander (Hemidactylium scutatum) larvae to test two models that predict a larva’s age and size at metamorphosis. The Wilbur-Collins model proposes that the developmental rate of a larva responds to changes in growth rate in an adaptive manner throughout the larval period, and that metamorphosis can be initiated after a minimum size has been reached. The Leips-Travis or fixed-rate model states that developmental rate is set early in the larval period, perhaps by early growth rate or food availability and their positive correlation with developmental rate, and that changes in growth rate during the larval period affect size at metamorphosis, but have no effect on the age of an individual at metamorphosis. A modified version of the Wilbur-Collins model suggests that a larva’s developmental rate becomes fixed about two-thirds of the way through the larval period, with changes in growth rate after that point only affecting size at metamorphosis. Larvae were raised on eight different feeding regimes which created two constant and six variable growth histories. Growth history did significantly affect size at metamorphosis. However, an a posteriori statistical test revealed a group of seven and an overlapping group of six treatments with indistinguishable lengths of larval period, indicating a general picture of a fixed developmental rate regardless of growth history. This result is unique among similar studies on invertebrates, fish, and frogs. There was no association between early growth or food level and development rates. Neither the Wilbur-Collins nor the Leips-Travis fixed-rate models were supported. The invariable developmental rate of Hemidactylium and recent osteological evidence from the literature suggest that larvae begin the process of metamorphosis as soon as they hatch, probably a trait selected for by strong predation pressure in the aquatic environment. A variety of different approaches (ecological, developmental, phylogenetic) are necessary to fully evaluate the adaptive nature of the timing of transitions between life cycle stages. Received: 3 June 1999 / Accepted: 18 March 2000     

Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles,songs, and habitat associations

North American field crickets (genus Gryllus) exhibit a diversity of life cycles, habitat associations, and calling songs. However, patterns of evolution for these ecological and behavioral traits remain uncertain in the absence of a robust phylogenetic framework. Analyses of morphological variation have provided few clues about species relationships in the genus Gryllus. Here we use comparisons of mitochondrial DNA restriction site maps for 29 individuals representing 11 species (including potential outgroups) to examine relationships among eastern North American field crickets. Initially chosen as likely outgroup taxa, the two European species of Gryllus do not obviously fall outside of an exclusively North American clade and (based on amount of sequence divergence) appear to have diverged from North American lineages at about the same time that major North American lineages diverged from each other. The egg-overwintering crickets comprise a strongly supported monophyletic group, but relationships among these three closely related species cannot be resolved. The mtDNA data are consistent with a single origin of egg diapause and do not support a model of recent life cycle divergence and allochronic speciation for Gryllus pennsylvanicus and G. veletis. The two crickets are not sister species, despite remarkable similarity in morphology, habitat, and calling song. This conclusion is consistent with published data on allozyme variation in North American field crickets. The habitat associations of eastern North American field crickets have been labile, but calling songs sometimes have remained virtually unchanged across multiple speciation events.     

Energy and the tempo of evolution in amphibians

Aim The evolutionary speed hypothesis (ESH) attempts to explain global patterns of species richness on the basis that rates of molecular evolution and speciation in warmer climates have led to a greater accumulation of taxa at lower latitudes. A substantial alternative hypothesis to the ESH is the tropical conservatism hypothesis (TCH). However, recent tests of the TCH, using amphibians as the model taxon, have relied on the assumption that rates of molecular evolution are stable across latitudes and elevations. Here, we test for the first time for systematic variation in rates of molecular evolution across latitude and elevation among amphibians. Location The dataset is geographically diverse with samples from all continents except Antarctica and also from many of the earth's major tropical–warm temperate archipelagos. Methods We tested for substitution rate heterogeneity across climatically varying habitats with the mitochondrial RNA genes 12S and 16S. Thus, we report here on our findings for amphibians – a taxon whose phylogenetic and trophic contexts are remote from those previously tested – using genes that have also not been examined before. The study utilized paired contrasts of sister species (188 species across 18 families, including both caudates and anurans) that are spatially separated in either latitudinal or elevational dimensions. Results We found substantially faster substitution rates for species living in warmer habitats (P= 0.001–0.002) at both lower latitudes (P < 0.02) and lower elevations (P < 0.01). Main conclusions The consistency of these results with the previous studies that used quite different organisms – and in this instance also using different genes – suggests that this is a ubiquitous pattern in nature consistent with the predictions of the ESH. Recent tests of the TCH that, in estimating diversification rates, have relied on the assumption that DNA evolution occurs at a constant rate across latitudes and elevations, require reconsideration in light of the findings presented here. Our results indicate that greater caution is required when estimating dates of divergence using DNA sequence data.     

The trophic vacuum and the evolution of complex life cycles in trophically transmitted helminths

Parasitic worms (helminths) frequently have complex life cycles in which they are transmitted trophically between two or more successive hosts. Sexual reproduction often takes place in high trophic-level (TL) vertebrates, where parasites can grow to large sizes with high fecundity. Direct infection of high TL hosts, while advantageous, may be unachievable for parasites constrained to transmit trophically, because helminth propagules are unlikely to be ingested by large predators. Lack of niche overlap between propagule and definitive host (the trophic transmission vacuum) may explain the origin and/or maintenance of intermediate hosts, which overcome this transmission barrier. We show that nematodes infecting high TL definitive hosts tend to have more successive hosts in their life cycles. This relationship was modest, though, driven mainly by the minimum TL of hosts, suggesting that the shortest trophic chains leading to a host define the boundaries of the transmission vacuum. We also show that alternative modes of transmission, like host penetration, allow nematodes to reach high TLs without intermediate hosts. We suggest that widespread omnivory as well as parasite adaptations to increase transmission probably reduce, but do not eliminate, the barriers to the transmission of helminths through the food web.     

The macroecology of population dynamics: taxonomic and biogeographic patterns in population cycles

Regular cycles in population abundance are fascinating phenomena, but are they common in natural populations? How are they distributed among taxa? Are there differences between different regions of the world, or along latitudinal gradients? Using the new Global Population Dynamics Database we analysed nearly 700 long (25 + years) time series of animal field populations, looking for large-scale patterns in cycles. Nearly 30% of the time series were cyclic. Cycle incidence varied among taxonomic classes, being most common in mammal and fish populations, but only in fish did cycle incidence vary among orders. Cycles were equally common in European and North American populations, but were more common in Atlantic fish than Pacific fish. The incidence of cycles increased with latitude in mammals only. There was no latitudinal gradient in cycle period, but cycle amplitude declined with latitude in some groups of fish. Even after considering the biases in the data source and expected type I error, population cycles seem common enough to warrant ecological attention.     

Evolution of the alternation of haploid and diploid phases in life cycles. II. Maintenance of the haplo-diplontic cycle

The relative duration of the haploid and the diploid phases during the reproductive cycle varies greatly between organisms. This paper addresses the question of the evolution of haploid, diploid, and haplo-diplontic life cycles. When the life span of haploid and diploid individuals is constant whatever their cycle, we show that the haplo-diplontic cycle has an advantage, which depends on the sex-ratio in anisogamous species and on the probability of fertilization in isogamous species. This is because meiosis and fertilization occur half as often in the haplo-diplontic cycle as in haploid or diploid cycles, for the same number of generations of individuals. This argument is demonstrated using a model which considers a genetic determination of the cycle, and fixed haploid and diploid fitnesses. The relevance of measures of fitness of haploid and diploid individuals in predicting the evolution of life cycles is discussed. Measures obtained in algae are compared with theoretical predictions.     

Directed molecular evolution: bridging the gap between genomics leads and commercial products

Agricultural crops, engineered to express transgenic traits, have been rapidly adopted by farmers since the initial commercialization of this technology in 1996. However, despite nearly 20 years of research in agricultural biotechnology, only two product categories have achieved commercial success: plants containing transgenes conferring tolerance to herbicides and plants containing insecticidal protein genes derived from Bacillus thuringensis. A number of transgenic concepts, while exhibiting promising phenotypes in laboratory experiments, have failed to generate commercially viable crops. Many of the leads produced by modern integrative approaches to understanding plant biology will need further optimization to deliver economically viable crops. Directed molecular evolution represents a powerful technology to optimize newly discovered leads towards product objectives. In this review, we show by example how directed molecular evolution can be used to develop enabling technologies for plant biologists; how genes can be optimized to generate improved input traits such as those conferring insect tolerance, disease control and herbicide tolerance; and how plant quality can be altered to improve yield, produce novel industrial feedstocks and improve nutritional qualities.     

Aspects of the study of the life cycles of Antarctic copepods

Different approaches to the study of life cycle strategies of Antarctic copepods are described in an attempt to shed new light on our present knowledge. To date, most studies were carried out on abundance, horizontal and vertical distribution and stage composition during different seasons and in various regions. Hence, the seasonal pictures had to be compiled from different years and sampling regions. The physiological method includes measurements on e.g. egg production, feeding, respiration and excretion rates, C:N and O:N ratios, lipid and protein contents. However, both physiological and biochemical data are still rare. Results of field observations are given in this paper for investigations conducted within the last 15 years in the eastern Weddell Sea, while data of physiological parameters are based on a broader geographical region. In the eastern Weddell Sea, eight copepod species account for about 95% of copepod abundance and for more than 80% of copepod biomass. Within the calanoids, the small species Microcalanus pygmaeus dominates by numbers with 66%, while the large species Calanoides acutus and Calanus propinquus comprise together 52% of the biomass. Species abundance is lowest in winter and highest in summer/autumn, however, seasonal changes in the abundance of M. pygmaeus are small and this species occurs in similar quantities throughout the year. All copepod species show a distinct seasonal vertical distribution pattern and they occur in upper water layers in summer, in contrast to the other seasons. However, the depth layers of maximum concentration differ between species. The ontogenetic vertical migration is most pronounced in C. acutus and relatively weak in C. propinquus. The age structure also shows seasonal differences with the youngest population observed in summer for C. acutus, C. propinquus, Ctenocalanus citer or autumn for Metridia gerlachei, whereas the M. pygmaeus population is oldest during summer. The youngest copepodite stage and the males are not always present in C. acutus and C. propinquus. In contrast, all developmental stages and both sexes occur throughout the year in M. gerlachei, M. pygmaeus and C. citer. Gonad maturation in the dominant calanoid species proceeds well before the onset of phytoplankton production in the eastern Weddell Sea. However, the highest portion of females with ripe gonads and hence highest egg production rates coincide with the productive period in spring and summer. In autumn, ovaries of the three larger species C. acutus, C. propinquus and M. gerlacheiare all spent. In contrast, the percentage of ripe females of the two smaller species, C. citer and M. pygmaeus, stays high in autumn. Egg production rates are highly variable within one region and species. Many copepods accumulate large depots of lipid, mainly wax esters. In contrast, five species (C. propinquus, C. simillimus, Euchirella rostromagna, Stephos longipes and Paralabidocera antarctica) almost exclusively synthesise triacylglycerols and not wax esters. The lipid content exhibits distinct seasonal patterns, and is highest in autumn. A seasonal difference is also obvious in metabolic activities with lowest rates during the dark season. The adaptation to the pronounced seasonality in the Southern Ocean differs greatly between copepod species, and most Antarctic copepods stay active during the dark season. Calanoides acutus seems to be the only true diapause species. Calculations of summer developmental rates and winter mortality rates of the large species C. acutus and C. propinquus suggest that both species have a 1-year life cycle with few females overwintering and probably spawning a second time. In contrast, a 2-year life cycle is more likely in R. gigas. However, life cycle durations of all species studied are still uncertain and regional differences are very probable.     

Genetic perspectives on northern population cycles: bridging the gap between theory and empirical studies

Many key species in northern ecosystems are characterised by high‐amplitude cyclic population demography. In 1924, Charles Elton described the ecology and evolution of cyclic populations in a classic paper and, since then, a major focus has been the underlying causes of population cycles. Elton hypothesised that fluctuations reduced population genetic variation and influenced the direction of selection pressures. In concordance with Elton, present theories concern the direct consequences of population cycles for genetic structure due to the processes of genetic drift and selection, but also include feedback models of genetic composition on population dynamics. Most of these theories gained mathematical support during the 1970s and onwards, but due to methodological drawbacks, difficulties in long‐term sampling and a complex interplay between microevolutionary processes, clear empirical data allowing the testing of these predictions are still scarce. Current genetic tools allow for estimates of genetic variation and identification of adaptive genomic regions, making this an ideal time to revisit this subject. Herein, we attempt to contribute towards a consensus regarding the enigma described by Elton almost 90 years ago. We present nine predictions covering the direct and genetic feedback consequences of population cycles on genetic variation and population structure, and review the empirical evidence. Generally, empirical support for the predictions was low and scattered, with obvious gaps in the understanding of basic population processes. We conclude that genetic variation in northern cyclic populations generally is high and that the geographic distribution and amount of diversity are usually suggested to be determined by various forms of context‐ and density‐dependent dispersal exceeding the impact of genetic drift. Furthermore, we found few clear signatures of selection determining genetic composition in cyclic populations. Dispersal is assumed to have a strong impact on genetic structuring and we suggest that the signatures of other microevolutionary processes such as genetic drift and selection are weaker and have been over‐shadowed by density‐dependent dispersal. We emphasise that basic biological and demographical questions still need to be answered and stress the importance of extensive sampling, appropriate choice of tools and the value of standardised protocols.     

The effects of the evolution of stoichiometry-related traits on population dynamics in plankton communities

Both ecological stoichiometry and the evolution of traits for energetic interactions such as prey protection and predatory efficiency are considered to be important aspects affecting population dynamics. However, no attempt has been made to examine the effect of the evolution of traits relating to stoichiometry. This study first examined the effects of the evolution of nutrient utilization traits (i.e., the minimum nutrient content of prey, the maximum nutrient uptake affinity of prey and the nutrient contents of predators) on population dynamics in a plankton community. When the evolution of these traits was assumed, the range of the nutrient loading conditions where the system became unstable was smaller than when the evolution was not assumed, but the range of the conditions for zooplankton extinction became larger. Furthermore, when the trade-offs (i.e. genetic correlation between the traits) were assumed, the system rarely became extinct and the range of the nutrient loading conditions where the system became stable became larger through evolution. Stable dynamics were caused by increasing uptake affinity through evolution, and zooplankton extinction was caused by decreasing the minimum content of limiting nutrients. Thus, our results suggest that the evolution of traits relating to stoichiometry can affect the dynamics of the systems, and the outcomes the dynamics change greatly depend on which traits can evolve.     

动物生活史进化理论研究进展

综述了生活史性状、生活史对策、权衡、适合度及进化种群统计学等动物生活史进化领域的进展。权衡是生活史性状之间相互联系的纽带,分为生理权衡与进化权衡。适合度是相对的,与个体所处的特定环境条件有关,性状进化与适合度之间关系紧密。适合度是生活史进化理论研究的焦点。探讨动物生活史对策的理论很多,影响最大的是MacArthur和Wilson提出的r对策及K对策理论。随年龄的增长,动物存活率及繁殖率逐步下降的过程,称为衰老;解释衰老的进化理论主要有突变-选择平衡假设和多效对抗假设。进化种群统计学将种群统计学应用于生活史进化研究,为探讨表型适合度的进化提供了有效的手段。将进化种群统计学、数量遗传学及特定种系效应理论进行整合,建立完整的动物生活史进化综合理论体系,是当代此领域的最大挑战。     

Life history of Xenodexia ctenolepis: implications for life history evolution in the family Poeciliidae

Xenodexia ctenolepis (Hubbs, 1950) is a uniquely asymmetrical species in the fish family Poeciliidae that is endemic to a remote region of Guatemala. In the present study, we describe its life history based on the dissection of 65 adult females from three different collections. We show that it is a livebearer, has superfetation, or the ability to carry multiple litters of young in different stages of development, and has matrotrophy, or placentation, which results in the dry mass of young at birth being three- to four-fold greater than the egg at fertilization. The size distribution of males is non-normal in a fashion that suggests a genetic polymorphism for age and size at maturity. Most phylogenies place Tomeurus gracilis as the sister taxon to the remaining members of the family Poeciliidae. Because Tomeurus is the sole egg-layer in the family, egg-laying is thought to represent the life history of the common ancestor. Because Xenodexia possesses three supposed derived traits (livebearing, superfetation and matrotrophy), this phylogenetic hypothesis suggests that Xenodexia has a highly derived life history with respect to other members of the family. By contrast, the most recent DNA-based phylogeny suggests Xenodexia is the sister taxon to the remainder of the family. If this proves to be true, it suggests that some or all of these life history traits may have been characteristic of the common ancestor to the family, then lost and re-evolved multiple times within the family.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 77–85.