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Data from: Reproductive sharing in relation to group and colony-level attributes in a cooperative breeding fish
- 负责人：
- DOI：
- doi:10.5061/dryad.rv5mg
- 摘要：
- The degree to which group members share reproduction is dictated by both within-group (e.g. group size and composition) and between-group (e.g. density and position of neighbours) characteristics. While many studies have investigated reproductive patterns within social groups, few have simultaneously explored how within-group and between-group social structure influence these patterns. Here, we investigated how group size and composition, along with territory density and location within the colony, influenced parentage in 36 wild groups of a colonial, cooperatively breeding fish Neolamprologus pulcher. Dominant males sired 76% of offspring in their group, whereas dominant females mothered 82% of offspring in their group. Subordinate reproduction was frequent, occurring in 47% of sampled groups. Subordinate males gained more paternity in groups located in high-density areas and in groups with many subordinate males. Dominant males and females in large groups and in groups with many reproductively mature subordinates had higher rates of parentage loss, but only at the colony edge. Our study provides, to our knowledge, the first comprehensive quantification of reproductive sharing among groups of wild N. pulcher, a model species for the study of cooperation and social behaviour. Further, we demonstrate that the frequency of extra-pair parentage differs across small social and spatial scales.
Data from: The SOS response increases bacterial fitness, but not evolvability, under a sublethal dose of antibiotic
- 负责人：
- DOI：
- doi:10.5061/dryad.rv766
- 摘要：
- Exposure to antibiotics induces the expression of mutagenic bacterial stress–response pathways, but the evolutionary benefits of these responses remain unclear. One possibility is that stress–response pathways provide a short-term advantage by protecting bacteria against the toxic effects of antibiotics. Second, it is possible that stress-induced mutagenesis provides a long-term advantage by accelerating the evolution of resistance. Here, we directly measure the contribution of the Pseudomonas aeruginosa SOS pathway to bacterial fitness and evolvability in the presence of sublethal doses of ciprofloxacin. Using short-term competition experiments, we demonstrate that the SOS pathway increases competitive fitness in the presence of ciprofloxacin. Continued exposure to ciprofloxacin results in the rapid evolution of increased fitness and antibiotic resistance, but we find no evidence that SOS-induced mutagenesis accelerates the rate of adaptation to ciprofloxacin during a 200 generation selection experiment. Intriguingly, we find that the expression of the SOS pathway decreases during adaptation to ciprofloxacin, and this helps to explain why this pathway does not increase long-term evolvability. Furthermore, we argue that the SOS pathway fails to accelerate adaptation to ciprofloxacin because the modest increase in the mutation rate associated with SOS mutagenesis is offset by a decrease in the effective strength of selection for increased resistance at a population level. Our findings suggest that the primary evolutionary benefit of the SOS response is to increase bacterial competitive ability, and that stress-induced mutagenesis is an unwanted side effect, and not a selected attribute, of this pathway.
Data from: Color vision varies more among populations than among species of live-bearing fish from South America
- 负责人：
- DOI：
- doi:10.5061/dryad.s0054
- 摘要：
- Background: Sensory Bias models for the evolution of mate preference place a great emphasis on the role of sensory system variation in mate preferences. However, the extent to which sensory systems vary across- versus within-species remains largely unknown. Here we assessed whether color vision varies in natural locations where guppies (Poecilia reticulata) and their two closest relatives, Poecilia parae and Poecilia picta, occur in extreme sympatry and school together. All three species base mate preferences on male coloration but differ in the colors preferred. Results: Measuring opsin gene expression, we found that within sympatric locations these species have similar color vision and that color vision differed more across populations of conspecifics. In addition, all three species differ across populations in the frequency of the same opsin coding polymorphism that influences visual tuning. Conclusions: Together, this shows sensory systems vary considerably across populations and supports the possibility that sensory system variation is involved in population divergence of mate preference.
Data from: Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments
- 负责人：
- DOI：
- doi:10.5061/dryad.s04ng
- 摘要：
- Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p<0.05) and broader optimum thermal window for aerobic scope (>3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multi-variate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.
Data from: Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry
- 负责人：
- DOI：
- doi:10.5061/dryad.s4f13
- 摘要：
- The classification of melanoma into four histological subtypes has been questioned regarding its clinical validity in providing relevant information for treatment for metastatic tumors. Specific genetic alterations are associated with particular clinical and histopathological features, suggesting that these could be helpful in refining existing melanoma classification schemes. We analyzed BRAF V600E mutated melanomas to explore the Reflectance confocal microscopy (RCM) utility as a screening aid in the evaluation of the most appropriate patients for genetic testing. Thus, 32 melanomas were assessed regarding their BRAF V600E mutational status. Experts blinded to dermoscopic images and V600E immunohistochemistry results evaluated RCM images regarding previously described melanoma features. BRAF positive melanomas were related to younger age (p=0.035), invasive melanomas (p=0.03) and to the presence of hiporreflective cells (p=0.02), epidermal nests (p=0.02), dermal-epidermal junction nests (p=0.05), edged papillae (p=0.05), and bright dots (p=0.05), and to absence of junctional thickening due to isolated cells (p=0.01) and meshwork (p=0.02). This study can not characterize other mutations in the BRAF, because the immunohistochemistry is specific to the type V600E. The findings should encourage the genetic evaluation of BRAF mutation. This study highlights the potential of RCM as a supplementary tool in the screening of BRAF-mutated melanomas.
Data from: Specialization and accuracy of host-searching butterflies in complex and simple environments
- 负责人：
- 关键词：
- Information processing;complexity;individual specialization;foraging;host preference;Pieris rapae
- DOI：
- doi:10.5061/dryad.s70m4
- 摘要：
- Populations that have access to a variety of resources are often composed of individuals that specialize on different subsets of resources. Understanding the behavioral mechanisms that drive such individual specialization will help us predict the strength of this specialization across different environments. Here, we explore the idea that individual specialization may be a consequence of constraints on an individual’s ability to process information. Because many environments contain an overwhelming number of resources and associated stimuli, individuals that specialize by focusing on only a subset of these resources may make more accurate decisions than individuals that generalize. Furthermore, we expect individuals in complex environments, where there are more resources and associated stimuli to process, to specialize during their search for resources compared to individuals in simple environments. We tested these predictions by measuring the accuracy and degree of specialization of na?ve cabbage white butterflies (Pieris rapae) searching for two target host species (radish and cabbage) in simple (one distractor species) and more complex (four distractor species) environments. Only butterflies that specialized on cabbage were more accurate than butterflies that visited a mixture of both radish and cabbage. Furthermore, na?ve butterflies searching for hosts in complex environments did not adopt more specialized foraging strategies than naive butterflies searching for hosts in simple environments. Taken together, these results suggest that the foraging benefits associated with specialization might only apply to certain resources (perhaps those that have readily recognizable cues) and that such specializations can be related to accuracy across multiple environments.
Data from: Evolutionary diversification of reef corals: a comparison of the molecular and fossil records
- 负责人：
- DOI：
- doi:10.5061/dryad.s7dj0
- 摘要：
- Understanding historical patterns of diversity dynamics is of paramount importance for many evolutionary questions. The fossil record has long been the only source of information on patterns of diversification, but the molecular record, derived from time-calibrated phylogenies, is becoming an important additional resource. Both fossil and molecular approaches have shortcomings and biases. These have been well studied for fossil data but much less so for molecular data and empirical comparisons between approaches are lacking. Here we compare the patterns of diversification derived from fossil and molecular data in scleractinian reef coral species. We also assess the robustness of molecular diversification rates to poor taxon sampling. We find that the temporal pattern of molecular diversification rates is robust to incomplete sampling when rates are calculated per interval. The major obstacle of molecular methods is that rate estimates are distorted because diversification rates can never be negative, whereas the fossil record suffers from incomplete preservation and inconsistent taxonomy. Nevertheless, the molecular pattern of diversification is comparable to the pattern we observe in the fossil record, with the timing of major diversification pulses coinciding in each dataset. For example, both agree that the end-Triassic coral extinction was a catastrophic bottleneck in scleractinian evolution.
Data from: Marine soundscape shaped by fishing activity
- 负责人：
- 关键词：
- DOI：
- doi:10.5061/dryad.s6f4q
- 摘要：
- Marine communities face anthropogenic pressures that degrade ecosystems. Because underwater soundscapes carry information about habitat quality, we explored whether destructive impacts of fishing could be evaluated via the soundscape. Maerl beds are recognized as biodiversity hotspots and they experience major worldwide degradation owing to fishing. We collected field acoustic recordings in maerl beds exposed to different fishing practices. We found that unfished maerl beds were threefold louder and exhibited sound frequencies more diversified than those recorded in fished maerl beds. Analyses of associated fauna samples indicated that snapping shrimps provided a major contribution to the maerl bed soundscape. Moreover, sea urchins and squat lobsters most likely contributed to differences between the soundscapes of unfished and fished maerl beds. Our results supported the idea that the soundscape can provide valuable information on maerl bed ecosystem health related to fishing activity.
Data from: Genetic variation in invasive species response to direct and indirect species interactions
- 负责人：
- DOI：
- doi:10.5061/dryad.s6n57
- 摘要：
- Biotic resistance to invasion arises from strong species interactions that decrease the fitness and population growth rates of potential invaders. Strong, direct interactions such as predation and competition are typically thought to drive biotic resistance, but in diverse communities, indirect interactions among species may also affect biotic resistance. Further, genetic variation in traits of the invading species that affect species interactions may allow some genotypes to overcome biotic resistance. We investigated the direct and indirect effects of a native legume (Acmispon wrangelianus) and insect herbivores on the fitness of different genotypes of an invasive legume (Medicago polymorpha) in a California grassland. Insect herbivores decreased Medicago fitness, but only in the presence of Acmispon, suggesting that indirect interactions mediated through insects and Acmispon are important for deterring Medicago invasion. Some Medicago genotypes were less affected by interactions with other species, however. This genetic variance suggests that while biotic resistance reduced the reproductive success of most genotypes, a few genotypes were able to overcome these complex interactions. However, Medicago invasion was unsuccessful in all treatments at several of our sites, suggesting that factors beyond those manipulated here also play a key role at many sites. At sites where biotic resistance is important, spatial and temporal variation in community composition and the genetic composition of the invasion pool may explain the invasion success of Medicago into this community.
Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data
- 负责人：
- 关键词：
- DOI：
- doi:10.5061/dryad.s71t4
- 摘要：
- Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.
