34 Works

Data from: Evolution of thorax architecture in ant castes highlights trade-off between flight and ground behaviors

Roberto A. Keller, Christian Peeters & Patrícia Beldade
The concerted evolution of morphological and behavioral specializations has compelling examples in ant castes. Unique to ants is a marked divergence between winged queens and wingless workers, but morphological specializations for behaviors on the ground have been overlooked. We analyzed thorax morphology of queens and workers in species from 21 of the 25 ant subfamilies. We uncovered unique skeletomuscular modifications in workers that presumably increase power and flexibility of head–thorax articulation, emphasizing that workers are...

Data from: Contribution of spatial heterogeneity in effective population sizes to the variance in pairwise measures of genetic differentiation

Jérôme G. Prunier, Vincent Dubut, Lounes Chikhi & Simon Blanchet
1. Pairwise measures of neutral genetic differentiation are supposed to contain information about past and on-going dispersal events and are thus often used as dependent variables in correlative analyses to elucidate how neutral genetic variation is affected by landscape connectivity. However, spatial heterogeneity in the intensity of genetic drift, stemming from variations in population sizes, may inflate variance in measures of genetic differentiation and lead to erroneous or incomplete interpretations in terms of connectivity. Here,...

Data from: Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity

Ricardo S. Ramiro, Henrique Costa & Isabel Gordo
Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP), and observed widespread...

Data from: Population divergence with or without admixture: selecting models using an ABC approach

Vitor C. Sousa, Mark A. Beaumont, Pedro Fernandes, Maria M. Coelho & Lounès Chikhi
Genetic data have been widely used to reconstruct the demographic history of populations, including the estimation of migration rates, divergence times and relative admixture contribution from different populations. Recently, increasing interest has been given to the ability of genetic data to distinguish alternative models. One of the issues that has plagued this kind of inference is that ancestral shared polymorphism is often difficult to separate from admixture or gene flow. Here, we applied an Approximate...

Data from: Genetic basis of stage-specific melanism: a putative role for a cysteine sulfinic acid decarboxylase in insect pigmentation

Patricia Beldade, Maria A. Jerónimo & Suzanne V. Saenko
Melanism, the overall darkening of the body, is a widespread form of animal adaptation to particular environments, and includes bookcase examples of evolution by natural selection, such as industrial melanism in the peppered moth. The major components of the melanin biosynthesis pathway have been characterized in model insects, but little is known about the genetic basis of life-stage specific melanism such as cases described in some lepidopteran species. Here, we investigate two melanic mutations of...

Data from: Positive epistasis drives the acquisition of multidrug resistance.

Sandra Trindade, Ana Sousa, Karina Bivar Xavier, Francisco Dionisio, Miguel Godinho Ferreira & Isabel Gordo
The evolution of multiple antibiotic resistance is an increasing global problem. Resistance mutations are known to impair fitness, and the evolution of resistance to multiple drugs depends both on their costs individually and on how they interact—epistasis. Information on the level of epistasis between antibiotic resistance mutations is of key importance to understanding epistasis amongst deleterious alleles, a key theoretical question, and to improving public health measures. Here we show that in an antibiotic-free environment...

Many ways to make darker flies: Intra- and inter-specific variation in Drosophila body pigmentation components

Elvira Lafuente, Filipa Alves, Jessica King, Carolina Peralta & Patrícia Beldade
Body pigmentation is an evolutionarily diversified and ecologically relevant trait with substantial variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution, including its ecological significance and genetic bases. Pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, and can be under different selective pressures. We decompose Drosophila thorax and abdominal...

Data from: The role of hermaphrodites in the experimental evolution of increased outcrossing rates in Caenorhabditis elegans

Sara Carvalho, Ivo M. Chelo, Christine Goy & Henrique Teotónio
Background: Why most organisms reproduce via outcrossing rather than selfing is a central question in evolutionary biology. It has long ago been suggested that outcrossing is favoured when it facilitates adaptation to novel environments. We have previously shown that the experimental evolution of increased outcrossing rates in populations of the male-hermaphrodite nematode Caenorhabditis elegans were correlated with the experimental evolution of increased male fitness. However, it is unknown whether outcrossing led to adaptation, and if...

Data from: Despite reproductive interference, the net outcome of reproductive interactions among spider mite species is not necessarily costly

Salomé H. Clemente, Inês Santos, Rita Ponce, Leonor R. Rodrigues, Susana A.M. Varela & Sara Magalhaes
Reproductive interference is considered a strong ecological force, potentially leading to species exclusion. This supposes that the net effect of reproductive interactions is strongly negative for one, or both, of the species involved. Testing this requires a comprehensive analysis of interspecific reproductive interactions, accounting for the order and timing of mating events, and for their effects on either fertility or fecundity. To this aim, we measured reproductive interactions among spider mites, using a focal species,...

Data from: Nutritional control of body size through FoxO-Ultraspiracle mediated ecdysone biosynthesis

Takashi Koyama, Marisa A. Rodrigues, Alekos Athanasiadis, Alexander W. Shingleton & Christen K. Mirth
Despite their fundamental importance for body size regulation, the mechanisms that stop growth are poorly understood. In Drosophila melanogaster, growth ceases in response to a peak of the molting hormone ecdysone that coincides with a nutrition-dependent checkpoint, critical weight. Previous studies indicate that insulin/insulin-like growth factor signaling (IIS)/Target of Rapamycin (TOR) signaling in the prothoracic glands (PGs) regulates ecdysone biosynthesis and critical weight. Here we elucidate a mechanism through which this occurs. We show that...

Data from: Evolution of longevity improves immunity in Drosophila

Daniel K. Fabian, Kathrin Garschall, Peter Klepsatel, Gonçalo Santos-Matos, Élio Sucena, Martin Kapun, Bruno Lemaitre, Robert Arking, Christian Schloetterer & Thomas Flatt
Much has been learned about the genetics of aging from studies in model organisms, but still little is known about naturally occurring alleles that contribute to variation in longevity. For example, analysis of mutants and transgenes has identified insulin signaling as a major regulator of longevity, yet whether standing variation in this pathway underlies microevolutionary changes in lifespan and correlated fitness traits remains largely unclear. Here we have analyzed the genomes of a set of...

Data from: Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

Miguel Carneiro, Stuart J. E. Baird, Sandra Afonso, Esther Ramirez, Pedro Tarroso, Henrique Teotonio, Rafael Villafuerte, Michael W. Nachman & Nuno Ferrand
Maintenance of genetic distinction in the face of gene flow is an important aspect of the speciation process. Here, we provide a detailed spatial and genetic characterization of a hybrid zone between two subspecies of the European rabbit. We examined patterns of allele frequency change for 22 markers located on the autosomes, X-chromosome, Y-chromosome, and mtDNA in 1078 individuals sampled across the hybrid zone. While some loci revealed extremely wide clines (w>=300 km) relative to...

Data from: The genetic basis and experimental evolution of inbreeding depression in Caenorhabditis elegans

Ivo M. Chelo, S. Carvalho, M. Roque, S. R. Proulx & Henrique Teotónio
Determining the genetic basis of inbreeding depression is important for understanding the role of selection in the evolution of mixed breeding systems. Here, we investigate how androdioecy (a breeding system characterized by partial selfing and outcrossing) and dioecy (characterized by obligatory outcrossing) influence the experimental evolution of inbreeding depression in Caenorhabditis elegans. We derived inbred lines from ancestral and evolved populations and found that the dioecious lineages underwent more extinction than androdioecious lineages. For both...

Data from: The fitness landscape of the codon space across environments

Inês Fragata, Sebastian Matuszweski, Mark A. Schmitz, Thomas Bataillon, Jeffrey D. Jensen & Claudia Bank
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino-acid...

Data from: Seasonal plasticity in anti-predatory strategies: matching of color and color preference for effective crypsis

Erik Van Bergen & Patricia Beldade
Effective anti-predatory strategies typically require matching appearance and behavior in prey, and there are many compelling examples of behavioral repertoires that enhance the effectiveness of morphological defenses. When protective adult morphology is induced by developmental environmental conditions predictive of future predation risk, adult behavior should be adjusted accordingly to maximize predator avoidance. While behavior is typically strongly affected by the adult environment, developmental plasticity in adult behavior — mediated by the same pre-adult environmental cues...

Data from: Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India

Sujeet Kumar Singh, Jouni Aspi, Laura Kvist, Reeta Sharma, Puneet Pandey, Sudhanshu Mishra, Randeep Singh, Manoj Agrawal & Surendra Prakash Goyal
Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial...

Short telomeres drive pessimistic judgment bias in zebrafish

Rui Oliveira, Felipe Espigares, Diana Abad, Miguel Godinho-Ferreira & Susana Varela
The role of telomerase reverse transcriptase (TERT) has been widely investigated in the contexts of aging and age-related diseases. Interestingly, decreased telomerase activities (and accelerated telomere shortening) have also been reported in patients with emotion-related disorders, opening the possibility for subjective appraisal of stressful stimuli playing a key role in stress-driven telomere shortening. In fact, patients showing a pessimistic judgment bias have shorter telomeres. However, these evidences in humans are correlational and the causal inference...

Data from: On the (un)predictability of a large intragenic fitness landscape

Claudia Bank, Sebastian Matuszewski, Ryan T. Hietpas & Jeffrey D. Jensen
The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness effects of mutations, allowing us to test theoretical predictions and improve our understanding of the shape of the true underlying fitness landscape and its implications for the predictability and repeatability of evolution. Here, we present a uniquely large multiallelic fitness landscape comprising...

Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B. Best, Ken P. Findlay, Salvatore Cerchio, Tim Collins, Marcia H. Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P. G. H. Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meӱer, Meredith Thornton & Howard C. Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample,...

Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range

Erwan Quéméré, Fabrice Hibert, Christian Miquel, Emeine Lhuillier, Emmanuel Rasolondraibe, Julie Champeau, Clément Rabarivola, Louis Nusbaumer, Cyrille Chatelain, Laurent Gautier, Patrick Ranirison, Brigitte Crouau-Roy, Pierre Taberlet, Lounès Chikhi & Emeline Lhuillier
In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to...

Data from: Coordination of wing and whole body development at developmental milestones ensures robustness against environmental and physiological perturbations

Marisa M. Oliveira, Alexander W. Shingleton & Christen K. Mirth
Development produces correctly patterned tissues under a wide range of conditions that alter the rate of development in the whole body. We propose two hypotheses through which tissue patterning could be coordinated with whole body development to generate this robustness. Our first hypothesis states that tissue patterning is tightly coordinated with whole body development over time. The second hypothesis is that tissue patterning aligns at developmental milestones. To distinguish between our two hypotheses, we developed...

Data from: Birth date predicts alternative life-history pathways in a fish with sequential reproductive tactics

Teresa Fagundes, Mariana G. Simões, João L. Saraiva, Albert F. H. Ros, David Gonçalves & Rui F. Oliveira
In species with plastic expression of alternative reproductive tactics (ARTs), individuals of the same sex, usually males, can adopt different reproductive tactics depending on factors such as body size. The ‘birth date hypothesis’ proposes that condition-dependent expression of ARTs may ultimately depend on birth date, because individuals born at different times of the year may achieve different sizes and express different reproductive tactics accordingly. However, this has rarely been tested. Here, we tested this hypothesis...

Dysbiosis individualizes fitness effect of antibiotic resistance in the mammalian gut

Isabel Gordo, Luís Cardoso, Paulo Paulo Durão & Massimo Amicone
The fitness cost of antibiotic resistance in the absence of antibiotics is crucial to the success of suspending antibiotics as a strategy to lower resistance. Here we show that after antibiotic treatment the cost of resistance within the complex ecosystem of the mammalian gut is personalized. Using mice as an in vivo model, we find that the fitness effect of the same resistant mutation can be deleterious in a host, but neutral or even beneficial...

Data from: Genetic variation for outcrossing among Caenorhabditis elegans isolates

Henrique Teotonio, Diogo Manoel & Patrick C. Phillips
The evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or...

Social learning by mate-choice copying increases dispersal and reduces local adaptation

Manuel Sapage, Susana A. M. Varela & Hanna Kokko
1. In heterogeneous environments, dispersal may be hampered not only by direct costs, but also because immigrants may be locally maladapted. While maladaptation affects both sexes, this cost may be modulated in females if they express mate preferences that are either adaptive or maladaptive in the new local population. 2. Dispersal costs under local adaptation may be mitigated if it is possible to switch to expressing traits of locally adapted residents. In a sexual selection...

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