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opencc-zeroDec 2018View details →

Data from: Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors

The impact of insecticide resistance in malaria vectors is poorly understood and quantified. Here a series of geospatial datasets for insecticide resistance in malaria vectors are provided so that trends in resistance in time and space can be quantified and the impact of resistance found in wild populations on malaria transmission in Africa can be assessed. Data are also provided for common genetic markers of resistance to support analyses of whether these genetic data can improve the ability to monitor resistance in low resource settings. Specifically, data have been collated and geopositioned for the prevalence of insecticide resistance, as measured by standard bioassays, in representative samples of individual species or species complexes. Data are provided for the Anopheles gambiae species complex, the Anopheles funestus subgroup, and for nine individual vector species. In addition, allele frequencies for known resistance associated markers in the Voltage-gated sodium channel (Vgsc) are provided. In total, eight analysis-ready, standardised, geopositioned datasets encompassing over 20,000 African mosquito collections between 1957 and 2017 are provided.

opencc-zeroDec 2013View details →

Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on FST values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.

opencc-zeroJun 2021View details →

Thermal adaptation in a holobiont accompanied by phenotypic changes in an endosymbiont

How and if organisms can adapt to changing temperatures has drastic consequences for the natural world. Thermal adaptation involves finding a match between temperatures permitting growth and the expected temperature distribution of the environment. However, if and how this match is achieved, and how tightly linked species change together, are poorly understood. Paramecium bursaria is a ciliate that has a tight physiological interaction with endosymbiotic green algae (zoochlorellae). We subjected a wild population of P. bursaria to a cold and warm climate (20℃ and 32℃) for ~300 generations. We then measured the thermal performance curve (TPC) for intrinsic rate of growth (rmax ) for these evolved lines across temperatures. We also evaluated number and size of the zoochlorellae populations within paramecia cells. TPCs for warm-adapted populations were shallower and broader than TPCs of cold-adapted populations, indicating that the warm populations adapted by moving along a thermal generalist/specialist trade off rather than right-shifting the TPC. Zoochlorellae populations within cold-adapted paramecia had fewer and larger zoochlorellae than hot-adapted paramecia, indicating phenotypic shifts in the endosymbiont accompany thermal adaptation in the host. Our results provide new and novel insight into how species involved in complex interactions will be affected by continuing increasing global temperatures.

opencc-zeroDec 2015View details →

Data from: Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress resistance-related enzyme activities during early life stages in Atlantic salmon

Oxidative stress (OS) may pose important physiological constraints on individuals, affecting trade-offs between growth and reproduction or ageing and survival. Despite such evolutionary and ecological importance, the results from studies on the magnitude of individual variation in OS resistance and the underlying causes of this variation such as genetic, environmental, and maternal origins, remain inconclusive. Using a high throughput methodology, we investigated the activity levels in three OS resistance-related enzymes (superoxide dismutase, SOD; glutathione reductase, GR; glutathione S-transferase, GST) during the early life stages of 1000 individuals from 50 paternal half-sib families in two populations of Atlantic salmon. Using animal mixed models, we detected the presence of narrow-sense heritability for SOD and GST; that for GST differed between populations due to differences in environmental variance. We found support for the presence of common environmental variation, including maternal effects, for only GR. Using a bivariate animal model, we detected a positive environmental correlation between activity levels of SOD and GST but were unable to detect an additive genetic correlation. Our results complement previous heritability findings for levels of reactive oxygen species or OS resistance by demonstrating the presence of heritability for OS-related enzyme activities. Our findings provide a foundation for future work, such as investigations on the evolutionary importance of variation in enzyme activities. In addition, our findings emphasise the importance of accounting for developmental stage, environmental variance, and kin relationships when investigating the OS-response at the enzyme activity level.

opencc-zeroDec 2012View details →

Data from: The effects of inbreeding, genetic dissimilarity and phenotype on male reproductive success in a dioecious plant

Pollen fate can strongly affect the genetic structure of populations with restricted gene flow and significant inbreeding risk. We established an experimental population of inbred and outbred Silene latifolia plants to evaluate the effects of (i) inbreeding depression, (ii) phenotypic variation and (iii) relatedness between mates on male fitness under natural pollination. Paternity analysis revealed that outbred males sired significantly more offspring than inbred males. Independently of the effects of inbreeding, male fitness depended on several male traits, including a sexually dimorphic (flower number) and a gametophytic trait (in vitro pollen germination rate). In addition, full-sib matings were less frequent than randomly expected. Thus, inbreeding, phenotype and genetic dissimilarity simultaneously affect male fitness in this animal-pollinated plant. While inbreeding depression might threaten population persistence, the deficiency of effective matings between sibs and the higher fitness of outbred males will reduce its occurrence and counter genetic erosion.

opencc-zeroDec 2016View details →

Data from: Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a "climate change" common garden, where we raised temperature 3°C, decreased pH by 0.2 units, and limited food supply by filtering out planktonic particles > 5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170,000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of > 90% when effective sample size is 900.

opencc-zeroDec 2016View details →

Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird

Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A. caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced-representation sequencing approach to generate a panel of 1,929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh, and coastal brackish-water marsh habitats. These patterns support the current species-level recognition but do not match the subspecies-level taxonomy within each species– a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.

opencc-by-4.0Jul 2021View details →

Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype (TEM data)

This is the TEM imaging data for the desmosome analysis as reported in the manuscript titled "Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype."

FIGURE 15 A–F in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 15 A–F: Stigonema parallelum. A: General aspect of a thallus. B–D: Parallel filaments. E: Branched filament. F: Filament forming a hormogonium. Scales: Scales: 10 µm.

FIGURE 14 A–R in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 14 A–R: Stigonema parallelum. A: Filament with a lateral heterocyte. B: Detail of filaments with lamellated sheaths. C–F: Parallel filaments forming hormogonia. G: Long filament with short branches. H–J: Details of apices. K: Germinating hormogonia. L–R: Development of filaments and releasing of hormogonia (life cycle). Scales: 10 µm in A (use for A, B), C (use for C–D), E, F (use for F–K) and L (use for L–R).

FIGURE 11 A–M in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 11 A–M: Stigonema corticola. A: General aspect of a thallus. B, C: Branched filaments. D: Young filament. E: Branches with agglomerated cells. F–H: Details of apex. I: Filament with a lateral heterocyte. J: Detail of a multiseriate filament. K: Initial stages of branching near the apex. L: Formation of hormogonium. M: Apex after releasing hormogonium. Scales: 10 µm in A (use for A, E), B (use for B–D), F (use for F–H), I and J (use for J–M).

FIGURE 10 A–F in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 10 A–F: Stigonema crassivaginatum. A: General aspect of a thallus. B–D: Details of branching. E: Detail of an apex. F: Lamellated sheaths. Scales: 50 µm in A and 10 µm in B–F.

FIGURE 12 A–I in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 12 A–I: Stigonema corticola. A: Uniseriate filament with lateral heterocyte. B–D: Mostly uniseriate filaments. E: Richly branched filaments. F–H: Agglomerated cells. I: Formation of a hormogonium. Scales: 10 µm in A (use for A–I).

FIGURE 9 A–H in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 9 A–H: Stigonema crassivaginatum. A: Branched filament with attenuated ends. B: Strictly uniseriate filaments. C: Formation of a hormogonium. D–F: Morphological variability of cells and apex. G: Sheaths with parallel lamellae. H: Sheaths with divergent lamellae. Scales: 10 µm in A (use for A–C), D (use for D–F) and G (use for G, H).

FIGURE 8 A–I in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 8 A–I: Stigonema tomentosum. A: Fasciculated filaments. B: Detail of biseriate filament. C: Detail of apex of branches. D: Branched filaments. E, F: Hormogonia. G: Initial stage of branching. H: Parallel erect branching. I: Branched uniseriate filaments. Scales: 10 µm A, B (use for B, C), D, E (use for E–H) and I.

FIGURE 7 A–F in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 7 A–F: Stigonema flexuosum. A: Detail of a biseriate filament. B: Branch after the release of a hormogonium. C: Branch forming a terminal hormogonium. D: Detail of a branch. E, F: Branched filaments with heterocytes. Scale: 10 µm in A (use for A–F).

FIGURE 6 A–E in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 6 A–E: Stigonema fremyi. A, B: General aspects of thallus. C–E: Details of attenuated branches. Scales: 10 µm in A, B, C (use for C–E).

FIGURE 5 A–F in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 5 A–F: Stigonema cf. minutum. A: General aspect of a thallus. B: Unilateral branching. C–D: Branches after releasing hormogonia. E–F: Details of main filaments. Scales: 10 µm.

FIGURE 4 A–J in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 4 A–J: Stigonema cf. minutum. A–G: General aspect of a thallus. H: Branches forming hormogonia at the ends. I: Young filament. J.: Detail of apex with epiphytic filament of Heteroleibleinia sp.. Scales: 10 µm A (use for A–D) and E–J.

FIGURE 2 A–N in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 2 A–N: Fischerella clavata. A–F: Details of widened apices of branches. G: Uniseriate main filament. H: Main filament with biseriate parts. I–K: Branching in main filaments. L–M: Hormogonia. N: Creeping filaments producing branch-like terminal filaments. Scale: 10 µm in A (use for A–N).