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77 results for “Selection bias”
Data from: Kin-bias, breeding site selection, and female fitness in a cannibalistic Neotropical frog
Resource availability influences sexual selection within populations and determines whether behaviours such as territoriality or resource sharing are adaptive. In Thoropa taophora, a frog endemic to the Atlantic Coastal Rainforest of Brazil, males compete for and defend limited breeding sites while females often share breeding sites with other females; however, sharing breeding sites may involve costs due to cannibalism by conspecific tadpoles. We studied a breeding population of T. taophora to determine (i) whether this species exhibits polygynous mating involving female choice for territorial males and limited breeding resources; (ii) whether limited breeding resources create the potential for male–male cooperation in defence of neighbouring territories; and (iii) whether females sharing breeding sites exhibit kin-biased breeding site choice, possibly driven by fitness losses due to cannibalism among offspring of females sharing sites. We used microsatellites to reconstruct parentage and quantify relatedness at eight breeding sites in our focal population, where these sites are scarce, and in a second population, where sites are abundant. We found that at localities where the appropriate sites for reproduction are spatially limited, the mating system for this species is polygynous, with typically two females sharing a breeding site with a male. We also found that females exhibit negative kin-bias in their choice of breeding sites, potentially to maximize their inclusive fitness by avoiding tadpole cannibalism of highly related kin. Our results indicate that male territorial defence and female site sharing are likely important components of this mating system, and we propose that kinship-dependent avoidance in mating strategies may be more general than previously realized.
Data from: Selection bias in mutation accumulation
<p>Mutation accumulation (MA) experiments, in which de novo mutations are sampled and subsequently characterized, are an essential tool in understanding the processes underlying evolution. In microbial populations, MA protocols typically involve a period of population growth between severe bottlenecks, such that a single individual can form a visible colony. While it has long been appreciated that the action of positive selection during this growth phase cannot be eliminated, it is typically assumed to be negligible. Here, we quantify the effect of both positive and negative selection in MA studies, demonstrating that selective effects can substantially bias the distribution of fitness effects (DFE) and mutation rates estimated from typical MA protocols in microbes. We then present a simple correction for this bias which applies to both beneficial and deleterious mutations, and can be used to correct the observed DFE in multiple environments. We use simulated MA experiments to illustrate the extent to which the MA-inferred DFE differs from the underlying true DFE, and demonstrate that the proposed correction accurately reconstructs the true DFE over a wide range of scenarios; we also provide an example of these corrections applied to experimental data. These results highlight that positive selection during microbial MA experiments is in fact not negligible, but can be corrected to gain a more accurate understanding of fundamental evolutionary parameters.</p>
Data from: Diversifying selection and color-biased dispersal in the asp viper
Background: The presence of intraspecific color polymorphism can have multiple impacts on the ecology of a species; as a consequence, particular color morphs may be strongly selected for in a given habitat type. For example, the asp viper (Vipera aspis) shows a high level of color polymorphism. A blotched morph (cryptic) is common throughout its range (central and western Europe), while a melanistic morph is frequently found in montane populations, presumably for thermoregulatory reasons. Besides, rare atypical uniformly colored individuals are known here and there. Nevertheless, we found in a restricted treeless area of the French Alps, a population containing a high proportion (>50%) of such specimens. The aim of the study is to bring insight into the presence and function of this color morph by (i) studying the genetic structure of these populations using nine microsatellite markers, and testing for (ii) a potential local diversifying selection and (iii) differences in dispersal capacity between blotched and non-blotched vipers. Results: Our genetic analyses support the occurrence of local diversifying selection for the non-blotched phenotype. In addition, we found significant color-biased dispersal, blotched individuals dispersing more than atypical individuals. Conclusion: We hypothesize that, in this population, the non-blotched phenotype possess an advantage over the typical one, a phenomenon possibly due to a better background matching ability in a more open habitat. In addition, color-biased dispersal might be partly associated with the observed local diversifying selection, as it can affect the genetic structure of populations, and hence the distribution of color morphs.
Data from: Females know better: sex-biased habitat selection by the European wildcat
The interactions between animals and their environment vary across species, regions, but also with gender. Sex‐specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex‐specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex‐specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use‐availability framework using radio‐telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid‐range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex‐biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex‐related differences in environmental preferences.
Raw fitness data (offspring number and weight), main dataset for manuscript: Female-specific resource limitation does not make the opportunity for selection more female biased
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Data from: The evolution of male-biased dispersal under the joint selective forces of inbreeding load, and demographic and environmental stochasticity
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Data from: A hidden Markov model to identify and adjust for selection bias: an example involving mixed migration strategies
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Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds
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Data from: Diversifying selection and color-biased dispersal in the asp viper
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Data from: Females know better: sex-biased habitat selection by the European wildcat
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Data from: Kin-bias, breeding site selection, and female fitness in a cannibalistic Neotropical frog
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Data from: The search for loci under selection: trends, biases and progress
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Data from: Selection bias in mutation accumulation
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Code and processed data accompanying "Widespread haploid-biased gene expression enables sperm-level natural selection"
<p>Code and processed data required to reproduce the analysis in "Widespread haploid-biased gene expression enables sperm-level natural selection".</p>
Data from: Sexual selection on male size drives the evolution of male-biased sexual size dimorphism via the prolongation of male development
Sexual size dimorphism (SSD) arises when the net effects of natural and sexual selection on body size differ between the sexes. Quantitative SSD variation between taxa is common, but directional intraspecific SSD reversals are rare. We combined micro- and macroevolutionary approaches to study geographic SSD variation in closely related black scavenger flies. Common garden experiments revealed stark intra and interspecific variation: Sepsis biflexuosa is monomorphic across the Holarctic, while S. cynipsea (only in Europe) consistently exhibits female-biased SSD. Interestingly, S. neocynipsea displays contrasting SSD in Europe (females larger) and North America (males larger), a pattern opposite to the geographic reversal in SSD of S. punctum documented in a previous study. In accordance with the differential equilibrium model for the evolution of SSD, the intensity of sexual selection on male size varied between continents (weaker in Europe) whereas fecundity selection on female body size did not. Subsequent comparative analyses of 49 taxa documented at least six independent origins of male-biased SSD in Sepsidae, which is likely caused by sexual selection on male size and mediated by bimaturism. Therefore, reversals in SSD and the associated changes in larval development might be much more common and rapid and less constrained than currently assumed.
Data from: Selection on structural allelic variation biases plasticity estimates
Wang and Althoff (2019) explored the capacity of Drosophila melanogaster to exhibit adaptive plasticity in a novel environment. In a full-sib, half-sib design, they scored the activity of the enzyme alcohol dehydrogenase (ADH) and plastic responses, measured as changes in ADH activity across ethanol concentrations in the range of 0-10% (natural variation) and 16% (the novel environment). ADH activity increased with alcohol concentration, and there was a positive association between larval viability and ADH activity in the novel environment. They also reported that families exhibiting greater plasticity had higher larval survival in the novel environment, concluding that ADH plasticity is adaptive. However, the four authors now concur that, since the study estimated plasticity from phenotypic differences across environments using full-sib families, it is not possible to disentangle the contributions of allele frequency changes at the Adh locus from regulatory control at loci known to influence ADH activity. Selective changes in allele frequencies may thus conflate estimates of plasticity; any type of "plasticity" (adaptive, neutral, or maladaptive) could be inferred depending on allele frequencies. The problem of scoring sib-groups after selection should be considered in any plasticity study that cannot use replicated genotypes. Researchers should monitor changes in allele frequencies as one mechanism to deal with this issue.
Data from: Mate finding, Allee effects, and selection for sex-biased dispersal
Although dispersal requires context-dependent decision-making in three distinct stages (emigration, transit, immigration), these decisions are commonly ignored in simple models of dispersal. For sexually reproducing organisms, mate availability is an important factor in dispersal decisions. Difficulty finding mates can lead to an Allee effect where population growth decreases at low densities. Surprisingly, theoretical studies on mate finding and on sex-biased dispersal produce opposing predictions: in the former one sex is predicted to move less if the other sex evolves to search more, whereas in the latter mate-finding difficulties can select for less sex bias in dispersal when mate finding occurs after dispersal. Here we develop a pair of models to examine the joint evolution of dispersal and settlement behaviour. Our first model resolves the apparent contradiction from the mate-search and dispersal literatures. Our second model demonstrates that the relationship between mating system and sex-biased dispersal is more complex than a simple contrast between resource-defence monogamy and female-defence polygyny. Our results highlight that a key factor is the timing of mating relative to dispersal (before, during, or after). We also show that although movement has the potential to alleviate a mate-finding Allee effect, in some cases it can actually exacerbate the effect.
Data from: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus – a long-time ecological model species – has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500 000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
Data from: Selection and sex-biased dispersal in a coastal shark: the influence of philopatry on adaptive variation
Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences of the mitochondrial control region in bonnethead sharks (Sphyrna tiburo), a species thought to exhibit female philopatry, collected from summer habitats used for gestation. Geographic patterns of mtDNA haplotypes and putatively neutral SNPs confirmed female philopatry and male-mediated gene flow along the northeastern coast of the Gulf of Mexico. A total of 30 outlier SNP loci were identified; alleles at over half of these loci exhibited signatures of latitude-associated selection. Our results indicate that in species with sex-biased dispersal, philopatry can facilitate sorting of locally adaptive variation, with the dispersing sex facilitating movement of potentially adaptive variation among locations and environments.
Variability in codon usage in Coronaviruses is mainly driven by mutational bias and selective constraints on CpG dinucleotide
<p>Supplementary Figures and Tables for the article called: " Variability in codon usage in Coronaviruses<em> </em>is mainly driven by mutational bias and selective constraints on CpG dinucleotide<sup>"</sup></p>
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