Browsing by Subject "NATURAL-SELECTION"

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  • Coronado-Zamora, Marta; Salvador-Martinez, Irepan; Castellano, David; Barbadilla, Antonio; Salazar-Ciudad, Isaac (2019)
    Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. melanogaster and Drosophila yakuba. For the set of genes expressed at different life-cycle stages of D. melanogaster, as reported in modENCODE, we estimate the ratio of substitutions relative to polymorphism between nonsynonymous and synonymous sites (alpha) and then alpha is discomposed into the ratio of adaptive (omega(a)) and nonadaptive (omega(na)) substitutions to synonymous substitutions. We find that the genes expressed in mid- and late-embryonic development are the most conserved, whereas those expressed in early development and postembryonic stages are the least conserved. Importantly, we found that low conservation in early development is due to high rates of nonadaptive substitutions (high omega(na)), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high omega(a)). By using estimates of different genomic features (codon bias, average intron length, exon number, recombination rate, among others), we also find that genes expressed in mid- and late-embryonic development show the most complex architecture: they are larger, have more exons, more transcripts, and longer introns. In addition, these genes are broadly expressed among all stages. We suggest that all these genomic features are related to the conservation of mid- and late-embryonic development. Globally, our study supports the hourglass pattern of conservation and adaptation over the life-cycle.
  • Lewis, Samuel H.; Salmela, Heli; Obbard, Darren J. (2016)
    Genetic studies of Drosophila melanogaster have provided a paradigm for RNA interference (RNAi) in arthropods, in which the microRNA and antiviral pathways are each mediated by a single Argonaute (Ago1 and Ago2) and germline suppression of transposable elements is mediated by a trio of Piwi-subfamily Argonaute proteins (Ago3, Aub, and Piwi). Without a suitable evolutionary context, deviations from this can be interpreted as derived or idiosyncratic. Here we analyze the evolution of Argonaute genes across the genomes and transcriptomes of 86 Dipteran species, showing that variation in copy number can occur rapidly, and that there is constant flux in some RNAi mechanisms. The lability of the RNAi pathways is illustrated by the divergence of Aub and Piwi (182-156Ma), independent origins of multiple Piwi-family genes in Aedes mosquitoes (less than 25Ma), and the recent duplications of Ago2 and Ago3 in the tsetse fly Glossina morsitans. In each case the tissue specificity of these genes has altered, suggesting functional divergence or innovation, and consistent with the action of dynamic selection pressures across the Argonaute gene family. We find there are large differences in evolutionary rates and gene turnover between pathways, and that paralogs of Ago2, Ago3, and Piwi/Aub show contrasting rates of evolution after duplication. This suggests that Argonautes undergo frequent evolutionary expansions that facilitate functional divergence.
  • Ohlund, Gunnar; Bodin, Mats; Nilsson, Karin A.; Ohlund, Sven-Ola; Mobley, Kenyon B.; Hudson, Alan G.; Peedu, Mikael; Brännström, Åke; Bartels, Pia; Prabel, Kim; Hein, Catherine L.; Johansson, Petter; Englund, Göran (2020)
    Lake-dwelling fish that form species pairs/flocks characterized by body size divergence are important model systems for speciation research. Although several sources of divergent selection have been identified in these systems, their importance for driving the speciation process remains elusive. A major problem is that in retrospect, we cannot distinguish selection pressures that initiated divergence from those acting later in the process. To address this issue, we studied the initial stages of speciation in European whitefish (Coregonus lavaretus) using data from 358 populations of varying age (26-10,000 years). We find that whitefish speciation is driven by a large-growing predator, the northern pike (Esox lucius). Pike initiates divergence by causing a largely plastic differentiation into benthic giants and pelagic dwarfs: ecotypes that will subsequently develop partial reproductive isolation and heritable differences in gill raker number. Using an eco-evolutionary model, we demonstrate how pike's habitat specificity and large gape size are critical for imposing a between-habitat trade-off, causing prey to mature in a safer place or at a safer size. Thereby, we propose a novel mechanism for how predators may cause dwarf/giant speciation in lake-dwelling fish species.
  • Mattila, Anniina L. K.; Jiggins, Chris D.; Opedal, Øystein H.; Montejo-Kovacevich, Gabriela; de Castro, Érika; McMillan, William O.; Bacquet, Caroline; Saastamoinen, Marjo (2021)
    Chemical defences against predators underlie the evolution of aposematic coloration and mimicry, which are classic examples of adaptive evolution. Surprisingly little is known about the roles of ecological and evolutionary processes maintaining defence variation, and how they may feedback to shape the evolutionary dynamics of species. Cyanogenic Heliconius butterflies exhibit diverse warning color patterns and mimicry, thus providing a useful framework for investigating these questions. We studied intraspecific variation in de novo biosynthesized cyanogenic toxicity and its potential ecological and evolutionary sources in wild populations of Heliconius erato along environmental gradients, in common-garden broods and with feeding treatments. Our results demonstrate substantial intraspecific variation, including detectable variation among broods reared in a common garden. The latter estimate suggests considerable evolutionary potential in this trait, although predicting the response to selection is likely complicated due to the observed skewed distribution of toxicity values and the signatures of maternal contributions to the inheritance of toxicity. Larval diet contributed little to toxicity variation. Furthermore, toxicity profiles were similar along steep rainfall and altitudinal gradients, providing little evidence for these factors explaining variation in biosynthesized toxicity in natural populations. In contrast, there were striking differences in the chemical profiles of H. erato from geographically distant populations, implying potential local adaptation in the acquisition mechanisms and levels of defensive compounds. The results highlight the extensive variation and potential for adaptive evolution in defense traits for aposematic and mimetic species, which may contribute to the high diversity often found in these systems.
  • Duplouy, Anne; Wong, Swee C.; Corander, Jukka; Lehtonen, Rainer; Hanski, Ilkka (2017)
    Background: Adaptation to local habitat conditions may lead to the natural divergence of populations in life-history traits such as body size, time of reproduction, mate signaling or dispersal capacity. Given enough time and strong enough selection pressures, populations may experience local genetic differentiation. The genetic basis of many life-history traits, and their evolution according to different environmental conditions remain however poorly understood. Methods: We conducted an association study on the Glanville fritillary butterfly, using material from five populations along a latitudinal gradient within the Baltic Sea region, which show different degrees of habitat fragmentation. We investigated variation in 10 principal components, cofounding in total 21 life-history traits, according to two environmental types, and 33 genetic SNP markers from 15 candidate genes. Results: We found that nine SNPs from five genes showed strong trend for trait associations (p-values under 0.001 before correction). These associations, yet nonsignificant after multiple test corrections, with a total number of 1,086 tests, were consistent across the study populations. Additionally, these nine genes also showed an allele frequency difference between the populations from the northern fragmented versus the southern continuous landscape. Discussion: Our study provides further support for previously described trait associations within the Glanville fritillary butterfly species across different spatial scales. Although our results alone are inconclusive, they are concordant with previous studies that identified these associations to be related to climatic changes or habitat fragmentation within the angstrom land population.
  • Byars, Sean G.; Huang, Qin Qin; Gray, Lesley-Ann; Bakshi, Andrew; Ripatti, Samuli; Abraham, Gad; Stearns, Stephen C.; Inouye, Michael (2017)
    Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.
  • Eriksson, Britas Klemens; Yanos, Casey; Bourlat, Sarah J.; Donadi, Serena; Fontaine, Michael C.; Hansen, Joakim P.; Jakubaviciute, Egle; Kiragosyan, Karine; Maan, Martine E.; Merilä, Juha; Austin, Åsa N.; Olsson, Jens; Reiss, Katrin; Sundblad, Göran; Bergström, Ulf; Eklöf, Johan S. (2021)
    Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. We studied the potential for niche differentiation between different plate armor phenotypes in a rapidly expanding population of a small prey fish, the three-spined stickleback (Gasterosteus aculeatus). In the central Baltic Sea, three-spined stickleback abundance has increased dramatically during the past decades. The increase in this typical mesopredator has restructured near-shore food webs, increased filamentous algal blooms, and threatens coastal biodiversity. Time-series data covering 22 years show that the increase coincides with a decline in the number of juvenile perch (Perca fluviatilis), the most abundant predator of stickleback along the coast. We investigated the distribution of different stickleback plate armor phenotypes depending on latitude, environmental conditions, predator and prey abundances, nutrients, and benthic production; and described the stomach content of the stickleback phenotypes using metabarcoding. We found two distinct lateral armor plate phenotypes of stickleback, incompletely and completely plated. The proportion of incompletely plated individuals increased with increasing benthic production and decreasing abundances of adult perch. Metabarcoding showed that the stomach content of the completely plated individuals more often contained invertebrate herbivores (amphipods) than the incompletely plated ones. Since armor plates are defense structures favored by natural selection in the presence of fish predators, the phenotype distribution suggests that a novel low-predation regime favors stickleback with less armor. Our results suggest that morphological differentiation of the three-spined stickleback has the potential to affect food web dynamics and influence the persistence and resilience of the stickleback take-over in the Baltic Sea.
  • Alho, Jussi S.; Leinonen, Tuomas; Merila, Juha (2011)
  • Zeng, Zhen; Sun, Hui; Vainio, Eeva J.; Raffaello, Tommaso; Kovalchuk, Andriy; Morin, Emmanuelle; Duplessis, Sebastien; Asiegbu, Fred O. (2018)
    Background: Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. Results: To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. Conclusion: Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.
  • Mohandesan, Elmira; Fitak, Robert R.; Corander, Jukka; Yadamsuren, Adiya; Chuluunbat, Battsetseg; Abdelhadi, Omer; Raziq, Abdul; Nagy, Peter; Stalder, Gabrielle; Walzer, Chris; Faye, Bernard; Burger, Pamela A. (2017)
    The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineage-specific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS
  • Rojas, Bibiana; Burdfield-Steel, Emily; De Pasqual, Chiara; Gordon, Swanne; Hernandez, Linda; Mappes, Johanna; Nokelainen, Ossi; Ronka, Katja; Lindstedt, Carita (2018)
    Chemically defended animals often display conspicuous color patterns that predators learn to associate with their unprofitability and subsequently avoid. Such animals (i.e., aposematic), deter predators by stimulating their visual and chemical sensory channels. Hence, aposematism is considered to be "multimodal." The evolution of warning signals (and to a lesser degree their accompanying chemical defenses) is fundamentally linked to natural selection by predators. Lately, however, increasing evidence also points to a role of sexual selection shaping warning signal evolution. One of the species in which this has been shown is the wood tiger moth, Arctia plantaginis, which we here put forward as a promising model to investigate multimodality in aposematic and sexual signaling. A. plantaginis is an aposematic diurnal moth which exhibits sexually dimorphic coloration as well as sex-limited polymorphism in part of its range. The anti-predator function of its coloration and, more recently, its chemical defenses (even when experimentally decoupled from the visual signals), has been well-demonstrated. Interestingly, recent studies have revealed differences between the two male morphs in mating success, suggesting a role of coloration in mate choice or attraction, and providing a possible explanation for its sexual dimorphism in coloration. Here, we: (1) review the lines of evidence showing the role of predation pressure and sexual selection in the evolution of multimodal aposematic signals in general, and in the wood tiger moth in particular; (2) establish gaps in current research linking sexual selection and predation as selective pressures on aposematic signals by reviewing a sample of the literature published in the last 30 years; (3) highlight the need of identifying suitable systems to address simultaneously the effect of natural and sexual selection on multimodal aposematic signals; and (4) propose directions for future research to test how aposematic signals can evolve under natural and sexual selection.
  • Johnson, Sini; Candolin, Ulrika (2017)
    Much evidence exists for sexually selected traits reflecting various components of mate quality, but the factors that limit signal expression and ensure honest signaling are less well known. Predation risk has been proposed to be one factor that could constrain the elaboration of visually conspicuous signals and ensure honesty, but little evidence exists because of limitations of earlier used methods. We investigated using a combination of field observations and experimental work if a conspicuous sexual signal of the threespine stickleback Gasterosteus aculeatus, the red nuptial coloration of the male, increases predation risk. We compared the proportion of colorful males in the gut of a predator in the wild, the perch Perca fluviatilis, to that in the population, and found proportionally more red-colored stickleback in the gut. This indicates that the predator selectively preys on colorful males under natural conditions. To differentiate between the effects of color and behavior on susceptibility to predation, we experimentally investigated the attack behavior of the predator towards breeding stickleback males differing in coloration. We found the predator to preferentially attack more colorful males, independent of their behavior. These results indicate that predation risk is a cost of the sexual signal that could limit expression and influence the honesty of the signal as an indicator of mate quality
  • Fountain, Toby Edward Soames; Nieminen, Marko Juhani; Siren, Jukka Pekka; Wong, Swee Chong; Lehtonen, Rainer Juhani; Hanski, Ilkka Aulis (2016)
    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.
  • Tringali, Angela; Bowman, Reed; Husby, Arild (2015)
    Sexually dimorphic plumage coloration is widespread in birds and is generally thought to be a result of sexual selection for more ornamented males. Although many studies find an association between coloration and fitness related traits, few of these simultaneously examine selection and inheritance. Theory predicts that sex-linked genetic variation can facilitate the evolution of dimorphism, and some empirical work supports this, but we still know very little about the extent of sex linkage of sexually dimorphic traits. We used a longitudinal study on juvenile Florida scrub-jays (Aphelocoma coerulescens) to estimate strength of selection and autosomal and Z-linked heritability of mean brightness, UV chroma, and hue. Although plumage coloration signals dominance in juveniles, there was no indication that plumage coloration was related to whether or not an individual bred or its lifetime reproductive success. While mean brightness and UV chroma are moderately heritable, hue is not. There was no evidence for sex-linked inheritance of any trait with most of the variation explained by maternal effects. The genetic correlation between the sexes was high and not significantly different from unity. These results indicate that evolution of sexual dimorphism in this species is constrained by low sex-linked heritability and high intersexual genetic correlation.
  • Brommer, Jon E.; Kontiainen, Pekka; Pietiäinen, Hannu (2012)
  • Morozov, Sergey; Leinonen, Tuomas; Merilä, Juha; McCairns, R. J. Scott (2018)
    Conspecifics inhabiting divergent environments frequently differ in morphology, physiology, and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate, and swimming performance in three-spined sticklebacks (Gasterosteus aculeatus L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the typical low-plated morph, and a unique small-plated morph. We test the hypothesis that similar to plate loss in other freshwater populations, reduction in lateral plate size also evolved in response to selection. Additionally, we test how morphology, physiology, and performance have evolved in concert as a response to differences in selection between marine and freshwater environments. We raised pure-bred second-generation fish originating from three populations and quantified their lateral plate coverage, burst- and critical swimming speeds, as well as standard and active metabolic rates. Using a multivariate Q(ST)-F-ST framework, we detected signals of directional selection on metabolic physiology and lateral plate coverage, notably demonstrating that selection is responsible for the reduction in lateral plate coverage in a small-plated stickleback population. We also uncovered signals of multivariate selection amongst all bivariate trait combinations except the two metrics of swimming performance. Divergence between the freshwater and marine populations exceeded neutral expectation in morphology and in most physiological and performance traits, indicating that adaptation to freshwater habitats has occurred, but through different combinations of traits in different populations. These results highlight both the complex interplay between morphology, physiology and performance in local adaptation, and a framework for their investigation.
  • Bajer, Katalin; Molnar, Orsolya; Török, Janos; Herczeg, Gabor (2012)
    Background Colour signals are widely used in intraspecific communication and often linked to individual fitness. The development of some pigment-based (e.g. carotenoids) colours is often environment-dependent and costly for the signaller, however, for structural colours (e.g. ultraviolet [UV]) this topic is poorly understood, especially in terrestrial ectothermic vertebrates. Methodology/Principal Findings In a factorial experiment, we studied how available energy and time at elevated body temperature affects the annual expression of the nuptial throat colour patch in male European green lizards (Lacerta viridis) after hibernation and before mating season. In this species, there is a female preference for males with high throat UV reflectance, and males with high UV reflectance are more likely to win fights. We found that (i) while food shortage decreased lizards' body condition, it did not affect colour development, and (ii) the available time for maintaining high body temperature affected the development of UV colour without affecting body condition or other colour traits. Conclusions/Significance Our results demonstrate that the expression of a sexually selected structural colour signal depends on the time at elevated body temperature affecting physiological performance but not on available energy gained from food per se in an ectothermic vertebrate. We suggest that the effect of high ambient temperature on UV colour in male L. viridis makes it an honest signal, because success in acquiring thermally favourable territories and/or effective behavioural thermoregulation can both be linked to individual quality.
  • Opedal, Øystein H.; Hegland, Stein Joar (2020)
    1. Pollinator-mediated reproductive interactions among co-flowering plant species are prime examples of how species interactions may affect fitness and community assembly. Despite considerable interest in these issues, statistical methods for assessing signal of reproductive interactions in observational data on co-flowering species are currently lacking. 2. We propose a flexible method for quantifying potential reproductive interactions among co-flowering plant species using the hierarchical latent-variable joint models implemented in the Hierarchical Modelling of Species Communities (HMSC) framework. The method accommodates any measure of reproductive success, including pollinator visitation, stigma pollen loads, and seed set. We demonstrate the method by analysing a dataset on bumblebee visitation to a set of co-flowering plant species in a species-rich meadow in Norway, and provide R tutorials for this and additional data types. 3. The example analysis revealed both positive and negative effects of heterospecific flower abundances on visitation to co-flowering species, which we interpret as potential reproductive interactions. 4. Synthesis. Hierarchical joint models provide a flexible approach to analysing patterns of covariation in the reproductive success of co-flowering species, thus identifying potential species interactions. Important strengths include explicit consideration of community-level effects and the assessment of residual fitness correlations after controlling for covariates such as flower abundances and phenotypic traits, yielding more complete insights into pollinator-mediated reproductive interactions.