A little sex goes a long way: clonal interference due to spatial structure can be alleviated by low rates of recombination
Author(s): Weissman, DB, Barton, NH
The spatial ranges over which populations occur are often much larger than the scales over which individuals migration and interact in a generation, and the resulting spatial structure can have large effects on adapting populations. In particular, the time for a beneficial allele to sweep through the population can be greatly increased if it must spread as a traveling wave over the whole range. It has recently been shown that the resulting increase in clonal interference limits the speed at which spatially-structured asexual populations can adapt, and that this limiting speed is much lower than that of well-mixed populations of the same size. We show that this is not the case for sexual populations: while the rate of adaptation is limited by interference, the limit on the adaptation of spatially-structured populations is not much lower than that on the adaptation of well-mixed ones. Even very low rates of recombination are sufficient to allow spatially-structured populations to adapt at speeds similar to well-mixed ones, suggesting that even organisms that are primarily asexual may be able to adapt fairly rapidly.
Department of Physics
A two-fold advantage of sex
Author(s): Park, S, Krug, J
The adaptation of large asexual populations is hampered by the competition between independently arising beneficial mutations in different individuals, which is known as clonal interference. In classic work, Fisher and Muller proposed that recombination provides an evolutionary advantage in large populations by alleviating this competition. Based on recent progress in quantifying the speed of adaptation in asexual populations undergoing clonal interference, we present a detailed analysis of the Fisher-Muller mechanism for a model genome consisting of two loci with an infinite number of beneficial alleles each and multiplicative (non-epistatic) fitness effects. We solve the deterministic, infinite population dynamics exactly and show that, for a particular, natural mutation scheme, the speed of adaptation in sexuals is twice as large as in asexuals. This result is argued to hold for any nonzero value of the rate of recombination. Guided by the infinite population result and by previous work on asexual adaptation, we postulate an expression for the speed of adaptation in finite sexual populations that agrees with numerical simulations over a wide range of population sizes and recombination rates. The ratio of the sexual to asexual adaptation speed is a function of population size that increases in the clonal interference regime and approaches 2 for extremely large populations. The simulations also show that recombination leads to a strong equalization of the number of fixed mutations in the two loci. The generalization of the model to an arbitrary number $L$ of loci is briefly discussed. For a particular communal recombination scheme, the ratio of the sexual to asexual adaptation speed is approximately equal to $L$ in large populations.
Adaptive evolution of the opsin genes in African crater lake cichlids?
Author(s): Musilova, Z, Albergati, L, Salzburger, W
Cichlid fishes from volcanic crater lakes represent small radiating lineages usually of few species. The Barombi Mbo Lake in Cameroon hosts a species flock of tilapiine cichlids, which underwent adaptive radiation similar to more famous Great Lakes cichlids. Several ecological adaptations were observed either in morphology of trophic apparatus (leading to feeding specializations) or extreme habitat preferences, such as deep-water niche. In general, cichlids are mainly visually oriented animals and their visual system shows in many cases the additional adaptations to the environment including the deep waters. Two ways of adaptation were found in cichlids from the Great Lakes, first in the DNA-sequence tuning and second in the gene expression levels differenciation. In the deep-water species convergently evolved mutations are known in opsin genes causing the shift of the chromophore sensitivity. The Barombi lake hosts a deep-water living species Konia dikume, however, nothing is known about the opsin evolution in these small crater lake systems so far. We sequenced a large region (up to 10 kbp) of each of the seven cone opsins (and putative regulatory regions) using the amplicon sequencing in the Ion Torrent next-generation sequencer. We further performed whole-transcriptome sequencing on the Ion Torrent next-generation sequencer to reconstruct robust phylogeny and we reconstruct evolution of the opsin genes by mapping on the tree. We further estimated the expression levels of all seven cone opsin genes, as well as the rod opsin. We found faster mutation rate in opsin genes in the genus Stomatepia (three species) and higher allelic variation within the genus Sarotherodon, however no DNA tuning has been found in Konia dikume.
Advantages of sex beyond recombination in a fungal model
Author(s): Schoustra, S, Debets, F, Giraud, T, Lopez-Villavicencio, M
Why sexual reproduction is so prevalent in nature remains a major question in evolutionary biology. Most of the proposed advantages of sex rely on the benefits obtained from recombination. However, it is still unclear whether the conditions under which these recombinatorial benefits would be sufficient to maintain sex in the short term are met in nature. Our study addresses a largely overlooked hypothesis, proposing that sex could be maintained in the short term by advantages due to functions associated with sex, but not related to recombination. These advantages would be so essential that sex could not be lost in the short term. Here, we used the fungus Aspergillus nidulans to experimentally test predictions of this hypothesis. Specifically, we were interested in (1) the short-term deleterious effects of recombination (2) possible non-recombinatorial advantages of sex particularly through the elimination of mutations, and (3) the outcrossing rate under choice conditions in a haploid fungus able to reproduce by both: outcrossing and haploid-selfing. Our results were consistent with the hypothesis: we found that 1) recombination can be strongly deleterious in the short term; 2) sexual reproduction between individuals derived from the same clonal lineage provided non-recombinatorial advantages likely through a selection arena mechanism.
Department of Biology
Artificial selection for host-plant use of a seed-predator: fitness consequences, inbreeding depression, and genetic variation
Author(s): Muola, A, Laukkanen, L, Leimu, R, Mutikainen, P
The use of alternative, suboptimal food-plant species affect herbivore’s fitness and life-history, and thus has both ecological and evolutionary consequences. Our study species, the seed predator Lygaeus equestris uses Vincetoxicum hirundinaria as its primary food plant. However, extensive spatio-temporal variation in seed production of V. hirundinaria occasionally enforces L. equestris to feed on alternative plant species. We conducted a long-term selection experiment to test if this seed predator is able to adapt to a suboptimal food-plant species in more than 20 generations. We measured fitness and adaptation in terms of increase in reproductive output. We replicated the populations within the selection lines to separate the effects of selection from random drift and conducted intra- and inter-population crosses to detect inbreeding and population differentiation. Furthermore, we analysed how population genetic structure changed during the selection experiment. We found that although the fitness of L. equestris that had fed on the alternative food plant was almost seven times lower than when feeding on V. hirundinaria, it increased significantly during the experiment indicating selection for higher fitness on the alternative food plant. Besides selection, random drift affected adaptation to the alternative food plant as indicated by differences in fitness among the replicate populations. Inter-population crosses within the selection lines resulted to higher fitness than intra-population crosses indicating inbreeding depression. To further underline the negative effects of random drift and inbreeding on adaptive potential of populations, we found that the level of genetic variation was lower in replicate populations feeding on the alternative food plant. Our study is novel in that it combines the analysis of population genetic structure to a more traditional selection experiment to examine host-plant specialization of herbivorous insects.
Genetics and Marine Biotechnology
Characteristic of Atlantic cod (Gadus morhua, L.) populations in the Baltic Sea according to its adaptations to local environmental changes
Author(s): Kijewska, A, Poćwierz-Kotus, A, Wenne, R
Atlantic cod (G. morhua, L.) presently is one of the most valuable commercial species in the Baltic Sea. Cod’s distribution in the Baltic Sea may depends on salinity and availability of spawning and feeding areas. Five samples of Baltic cod (n=150) were used for analyzing SNPs and genes expression. Data obtained for genes related to environmental conditions, e.g. salinity and temperature (alpha-enolase (Gm1156), heat-shock protein 90 (Hsp90), aromatase (Aro9), and neuropeptide Y (NPY)) show different distribution of alleles and suggest presence of minimum 2 populations of cod: eastern and western. The transitions area between those populations are correlated to decrease of salinity. The eastern stock is adapted to local environment, characterized by very low salinity (under 7 PSU). In fish from western Baltic Sea we observe higher genetic heterogeneity than in the eastern population, which has a very low admixture of alleles other than those correlated with low salinity. Western population is probably under strong influence of the North Sea cod’s stock. Further research should indicate if hypothesis assuming link between this differentiation and influence of local adaptations of cod is valid.
Santé des Plantes et Environnement
Clinal analysis of a temporary contact zone between two invading outbreaks to estimate dispersal of a major pest of maize
Author(s): Bermond, G, Blin, A, Vercken, E, Ravigné, V, Rieux, A, Mallez, S, Morel-Journel, T, Guillemaud, T
Dispersal is a key parameter involved in invasion, persistence and evolution of species. Despite the interest of obtaining dispersal estimates, measuring dispersal remains a real challenge due to its complexity and associated technical constraints. Some biological invasions may, however, be useful to estimate the dispersal. The western corn rootworm (WCR), Diabrotica virgifera virgifera, is one of the most destructive pests of corn and is invading Europe. The two main European invasive outbreaks of WCR are located in North-Western Italy and Central Europe and they originated from independent introductions from North America. Recently it was demonstrated that a secondary contact probably occurred between these two expanding outbreaks in 2008, in Northern Italy and led to the formation of an admixture zone. Here, we exploit this ongoing process to infer the dispersal of the WCR by analysing temporary frequency clines at 13 microsatellite markers. A measure of the clines slope and the linkage disequilibrium between microsatellites at the centre of the contact zone provided two estimates of WCR dispersal. Simulations with various non Gaussian dispersal kernels and population density heterogeneity in space showed that these estimations are robust to several deviations from the diffusion approximation. The order of magnitude of this estimation is then compared to others estimates of WCR dispersal and is discussed in the context of biological invasions. We conclude that secondary contacts between colonizing populations, which are common in invasive species, are very useful and could be used to infer dispersal parameters in many species.
Comparing evolvabilities: common errors surrounding the calculation and use of coefficients of additive genetic variation
Author(s): Garcia-Gonzalez, F, Simmons, LW, Tomkins, JL, Kotiaho, JS, Evans, JP
Evolvability, the ability of populations to respond to natural or sexual selection, is contingent on the level of additive genetic variation underlying trait expression. Two valuable evolvability measures are the coefficient of additive genetic variation (CVA) and its square (IA), which standardize the additive genetic variance by the mean of the trait and therefore allow comparisons among traits and taxa. CVA has been used widely to compare patterns of genetic variation. However, the utility of CVAs relies critically on the correct calculation of this parameter. We reviewed a sample of quantitative genetic studies, focusing on full sib-half sib breeding designs, and found that 45% of studies use incorrect methods for calculating CVA and that practices that render these coefficients meaningless are frequent. This is likely to compromise studies that use such statistics for comparative purposes. Our results are suggestive of a broader problem because miscalculation of the additive genetic variance from a sire model is prevalent among the studies sampled, implying that other important quantitative genetic parameters might also often be estimated incorrectly. Here we outline some issues affecting the use of CVA and IA, including scale effects, data transformation, and the comparison of traits with different dimensions. We also compile general guidelines for calculating, reporting and interpreting these evolvability measures in future studies.
Department of Biology
Comparison of Haplotype Methods to detect selection
Author(s): Vatsiou, A, MeLo De Lima, C, Gaggiotti, O
Motivation: The main topic of research in human genetics is the identification of genes and mutations that contribute to a genetic disease. One of the factors that can influence the genetic diversity in a population is natural selection. In this work, we will compare the existing long-range haplotype methods to detect selection. Our primary objective is to obtain a clear view about their power and validity under complex demographic scenarios. Methods & Results: Literature review: A systematic review that was conducted revealed five haplotype methods with available software to identify loci that have undergone selection. The five methods are the following: LRH (Sabeti, 2002; Nature 419:832-837), iHS (Voight, 2006; PLos Biol 4:72), xp-EHH (Sabeti, 2007; Nature 449:913-8), EHHST (Zhong, 2010; Hum Genet 18:1148-59) and xp-EHHST (Zhong, 2011; Stat & Its Interface 4:51–63). All of them used simulations to test their performance with the ms (Hudson, 2002; Bioinf 18:337-8) and SelSim programs (Spencer, 2004; Bioinf 20:3673-5). Sensitivity Analysis: Ms program can consider different demographic models, without selection and SelSim provides simulations under natural selection with a simple population structure. To determine the best method, we will generate simulated data using SimuPOP. SimuPOP is a forward-in-time simulation program that can construct models with selection under complex evolutionary scenarios. We will begin with an island model, a stepping stone model incorporating an environmental gradient and more complex scenarios including a hierarchically structured population. Conclusions: We will thoroughly investigate their behavior under complex scenarios. Our study sets the basis to identify the advantages and disadvantages of each method under each modeling assumption. Here, we restrict ourselves to the comparison of the methods but an extension to a model to detect selection to N populations could be developed at a later stage.
School of Earth and Environmental Sciences
Could rapid adaptation be contributing to the success of invasive Senecio madagascariensis in Australia? Combining outlier and spatial analysis methods to detect putative selection
Author(s): Dormontt, EE, Lowe, AJ
Identifying contemporary evolution is a major goal in invasion biology. A first step in this endeavour is to identify loci which may have been subject to recent selection and show associations with particular environmental conditions. Here we used 164 amplified fragment length polymorphism (AFLP) loci to carry out genome scans on a total of 316 individual Senecio madagascariensis plants collected from across the known invaded range in Australia. Half of these (n = 158) were collected from eight populations and the remainder collected as individual plants >2 km apart. The population and individual based samples were analysed separately using two complementary approaches for identifying putative loci under selection. Populations were analysed using outlier approaches in two programs MCHEZA and BAYESCAN; individuals were analysed using a spatial analysis method in SAM to look for associations between particular loci and environmental variables. Two loci were identified in both datasets as potentially under selection and were associated with monthly environmental variables describing light and water availability between May and August which corresponds with flowering time. Overall 6% of loci were identified as candidates for selection in one or more of the analysis methods, all three software programs only agreed on a single locus (0.6% of all loci) and this was associated with eight environmental parameters describing rainfall. Results are discussed with reference to selection and alternative explanations for the observed patterns. The two identified loci present promising targets for future investigations into contemporary selection in invasive S. madagascariensis in Australia.