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Phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment

This dataset contains phenotypic, genetic, and epigenetic data from 29 Serratia marcescens strains from an evolution experiment. In a previous study (https://doi.org/10.1111/evo.12148), the bacterium S. marcescens was left to evolve from a common ancestor culture in replicated populations kept under different temperature regimes, and evolved clones were isolated and their phenotypes measured. Here, we randomly selected 28 evolved clones from this experiment, as well as the original reference strain, and used PacBio single molecule real-time (SMRT) sequencing to obtain genetic and epigenetic (N6-methyladenine modifications, m6A) data. The goal of our study was to obtain a detailed description of the methylation landscape of S. marcescens and to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation.

opencc-by-4.0Mar 2007View details →

Figure 6 in Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)

Figure 6. One song strophe of Cettia a. concolor, Taiwan, May; tape recording by Per Alström.

Figure 4. Tree 1 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 4. Tree 1 rooted with the Viverridae (intergeneric analysis).

Figure 5. Tree 2 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 5. Tree 2 rooted with the Herpestidae (intergeneric analysis).

Figure 8 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 8. Phylogenetic relationships within the Genetta spp. clade (intrageneric analysis).

Figure 7. Tree 4 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 7. Tree 4 rooted both with the Felidae and the Canidae (intergeneric analysis).

Figure 6. Tree 3 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 6. Tree 3 rooted with the Felidae (intergeneric analysis).

Figure 11 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 11. Phylogenetic relationships within the genus Genetta, illustrating biotope distribution.

Figure 10 in Genets and 'genet-like' taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

Figure 10. Evolution of the metatarsal pads within the Genetta johnstoni + Prionodon clade.

Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of ex-situ and in-situ populations of B. insularis using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex-situ and in-situ populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the in-situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in-situ one, which is crucial for considering a reintroduction process into the island.

Genetic differentiation underlies seasonal variation in thermal tolerance, body size, and plasticity in a short-lived copepod

Organisms experience variation in the thermal environment on several different temporal scales, with seasonality being particularly prominent in temperate regions. For organisms with short generation times, seasonal variation is experienced across, rather than within, generations. How this variation affects the seasonal evolution of thermal tolerance and phenotypic plasticity is understudied, but has direct implications for the thermal ecology of these organisms. Here we document intra-annual patterns of thermal tolerance in two species of Acartia copepods (Crustacea) from a highly seasonal estuary, showing strong variation across the annual temperature cycle. Common garden, split-brood experiments indicate that this seasonal variation in thermal tolerance, along with seasonal variation in body size and phenotypic plasticity, is likely affected by genetic polymorphism. Our results show that adaptation to seasonal variation is important to consider when predicting how populations may respond to ongoing climate change.

Data from: Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola

Understanding the genetic basis of species differences is a major goal in evolutionary biology. Pigmentation divergence between Drosophila species often involves genetic changes in pigmentation candidate genes that pattern the body and wings, but it remains unclear how these changes affect pigmentation evolution in multiple body parts between the same diverging species. Drosophila elegans and D. gunungcola show pigmentation differences in the thorax, legs, and wings, with D. elegans exhibiting male-specific wing spots and D. gunungcola lacking wing spots with intensely dark thoraces and legs. Here, we performed QTL mapping to identify the genetic architecture of these differences. We find a large effect QTL on the X chromosome for all three body parts. QTL on Muller Element E were found for thorax pigmentation in both backcrosses but were only marginally significant in one backcross for the legs and wings. Consistent with this observation, we isolated the effects of the Muller Element E QTL by introgressing D. gunungcola alleles into a D. elegans genetic background and found that D. gunungcola alleles linked near the pigmentation candidate gene ebony caused intense darkening of the thorax, minimal darkening of legs, and minimal shrinking of wing spots. D. elegans ebony mutants showed changes in pigmentation consistent with Ebony having different effects on pigmentation in different tissues. Our results suggest that multiple genes have evolved differential effects on pigmentation levels in different body regions.

Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity

Carcinus maenas is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing. Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R). Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.

Genetics of mercury accumulation in Stickleback, genotypes and metal accumulation phenotypes

Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome wide association study (GWAS) between 28,450 SNPs and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs (Single Nucleotide Polymorphism) suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kbp distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback.

Colony fitness increases in the honey bee at queen mating frequencies higher than genetic diversity asymptote

Abstract Across the eusocial Hymenoptera, a queen's mating frequency is positively associated with her workers' genetic diversity and colony's fitness. Over 90% of a colony's diversity potential is achieved by its mother's tenth effective mating (me); however, many females mate at levels of me > 10, a zone we here call hyperpolyandry. We compared honey bee colony fitness at mating levels near and above this genetic diversity asymptote. We were interested in how hyperpolyandry affects colony phenotypes arising from both common tasks (brood care) and rare specialized tasks (parasite resistance). We used an unselected wild line of bees and a Varroa Sensitive Hygiene (VSH) line selected to resist the parasite Varroa destructor. Virgin queens were instrumentally inseminated to replicate the following queen/colony conditions: (1) VSH semen/low polyandry (observed mating number = mo = 9), (2) VSH semen/high polyandry (mo = 54), (3) wild type semen/low polyandry, or (4) wild semen/high polyandry. There was a positive effect of polyandry on brood survival, an outcome of common tasks, with highest values at mo = 54. There was an interaction between polyandry and genetics such that differences between genetic lines expressed only at mo = 54, with fewer mites in VSH colonies. These results are consistent with two hypotheses for the evolution of mating levels in excess of the genetic diversity asymptote: hyperpolyandry improves colony fitness by (1) optimizing genotype compositions for common tasks and (2) by capturing rare specialist allele combinations, resisting cliff-edge ecological catastrophes. Significance statement Polyandry is a female's practice of mating with several males, storing their sperm, and using it to produce one or more clutches of genetically diverse offspring. In the social Hymenoptera, polyandry increases the genetic diversity and task efficiency of workers, leading to improved colony fitness. Over 90% of the increase in a colony's diversity potential is achieved by its mother's tenth mating; however, many females practice hyperpolyandry, a term we reserve here for mating levels above this genetic diversity asymptote. We show that a token of colony fitness arising from common tasks, brood survival, improves universally as one moves from sub- to hyperpolyandrous mating levels. However, a colony phenotype arising from a rare parasite resistance task is only expressed in the presence of the controlling alleles and under conditions of hyperpolyandry. These results suggest adaptive mechanisms by which hyperpolyandry could evolve.

Genetic and ecomorphological divergence between sympatric Astyanax morphs from Central America

Intraspecific ecological and morphological polymorphism can promote ecological speciation and the build-up of reproductive isolation. Here, we evaluate correlations among morphology, trophic ecology, and genetic differentiation between two divergent morphs (elongate and deep-body) of the fish genus Astyanax in the San Juan River basin in Central America, to infer the putative evolutionary mechanism shaping this system. We collected the two morphs from three water bodies and analyzed: 1) the correlation between body shape and the shape of the premaxilla, a relevant trophic morphological structure, 2) the trophic level and niche width of each morph, 3) the correspondence between trophic level and body and premaxillary shape, and 4) the genetic differentiation between morphs using mitochondrial and nuclear markers. We found a strong correlation between the body and premaxillary shape of the morphs. The elongate-body morph had a streamlined body, a premaxilla with acuter angles and a narrower ascending process, and a higher trophic level, characteristic of species with predatorial habits. By contrast, the deep-body morph had a higher body depth, a premaxilla with less acute angles, and a broader trophic niche, suggesting generalist habits. Despite the strong correlation between morphological and ecological divergence, the morphs showed limited genetic differentiation, supporting the idea that morphs may be undergoing incipient ecological speciation, although alternative scenarios such as stable polymorphism or plasticity should also be considered. This study provides support for the role of ecological factors promoting diversification in lake and stream-dwelling freshwater fish.

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events vs. postformational mutation to patterns of genetic diversity in nature. Here we use restriction site associated DNA genotyping to evaluate genetic diversity and demographic history in Aspidoscelis laredoensis, a diploid unisexual lizard species from the vicinity of the Rio Grande River in southern Texas and northern Mexico. The sexual progenitor species from which one or more lineages are derived also occur in the Rio Grande Valley region, although patterns of distribution across individual sites are quite variable. Results from population genetic and phylogenetic analyses resolved the major axes of genetic variation in this species and highlight how these match predictions based on historical patterns of hybridization. We also found discordance between results of demographic modelling using different statistical approaches with the genomic data. We discuss these insights within the context of the ecological and evolutionary mechanisms that generate and maintain lineage diversity in unisexual species. As one of the most dynamic, intriguing, and geographically well investigated groups of whiptail lizards, these species hold substantial promise for future studies on the constraints of diversification in unisexual vertebrates.

Data from: Larval development in the Pacific oyster and the impacts of ocean acidification: differential genetic effects in wild and domesticated stocks

The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~ 400 µatm) and high (~ 1600 µatm) pCO2 conditions, both in domesticated and naturalized 'wild' oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early "D-stage" larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~ 26% fewer loci with changing allele frequencies across developmental stages and < 50% as many loci affected by acidified culture conditions, compared to larvae from wild brood stock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

Genetic differences in the temporal and environmental stability of transgenerational environmental effects

Environments influence the expression of phenotypes of individuals, their progeny, and even their grandprogeny. The duration of environmental effects and how they are modified by subsequent environments are predicted to be targets of natural selection in variable environments. However, little is known about the genetic basis of the temporal persistence of environmental effects and their stability of expression across subsequent environments, or even the extent to which natural genotypes differ in these attributes of environmental effects. We factorially manipulated the thermal environment experienced in three successive generations, to quantify the temporal persistence and environmental stability of temperature effects in contrasting genotypes of Arabidopsis thaliana. We found that genotypes differed in the manner in which environmental effects dissipated across successive generations, the manner in which responses to ancestral environments were stably expressed in present environments, the manner in which ancestral environments altered responses to present environments, and in the manner in which ancestral environments altered fitness in present conditions. Genetic variation exists in nature for these trait-specific environmental responses, suggesting that the temporal persistence and stability of environmental effects in variable environments have the potential to evolve in response to natural selection imposed by different environments and sequences of environments.