Changes In Genotype Frequencies Research Articles

Global Frequency Analyses of Canine Progressive Rod-Cone Degeneration-Progressive Retinal Atrophy and Collie Eye Anomaly Using Commercial Genetic Testing Data.

Hundreds of genetic variants associated with canine traits and disorders have been identified, with commercial tests offered. However, the geographic distributions and changes in allele and genotype frequencies over prolonged, continuous periods of time are lacking. This study utilized a large set of genotypes from dogs tested for the progressive rod-cone degeneration-progressive retinal atrophy (prcd-PRA) G>A missense PRCD variant (n = 86,667) and the collie eye anomaly (CEA)-associated NHEJ1 deletion (n = 33,834) provided by the commercial genetic testing company (Optigen/Wisdom Panel, Mars Petcare Science & Diagnostics). These data were analyzed using the chi-square goodness-of-fit test, time-trend graphical analysis, and regression modeling in order to evaluate how test results changed over time. The results span fifteen years, representing 82 countries and 67 breeds/breed mixes. Both diseases exhibited significant differences in genotype frequencies (p = 2.7 × 10-152 for prcd-PRA and 0.023 for CEA) with opposing graphical trends. Regression modeling showed time progression to significantly affect the odds of a dog being homozygous or heterozygous for either disease, as do variables including breed and breed popularity. This study shows that genetic testing informed breeding decisions to produce fewer affected dogs. However, the presence of dogs homozygous for the disease variant, especially for prcd-PRA, was still observed fourteen years after test availability, potentially due to crosses of unknown carriers. This suggests that genetic testing of dog populations should continue.

Fitness costs in the presence and absence of insecticide use explains abundance of two common Aedes aegypti kdr resistance alleles found in the Americas.

Aedes aegypti is the vector of viruses such as chikungunya, dengue, yellow fever and Zika that have a critical impact on human health. Control of adult mosquitoes is widely done using pyrethroids, but resistance has reduced the effectiveness of this class of insecticides. Resistance to pyrethroids in mosquitoes is commonly due to mutations in the voltage-gated sodium channel (Vgsc) gene (these mutations are known as knockdown resistance, kdr). In the Americas and the Caribbean, the most common kdr alleles are 410L+1016I+1534C and 1534C. In this study, we conducted a population cage experiment to evaluate changes in the allele and genotype frequencies of the 410L+1016I+1534C allele by crossing two congenic strains; one carrying the 410L+1016I+1534C and another with the 1534C allele. Changes in allele frequencies were measured over 10 generations in the absence of insecticide exposure. We also applied one cycle of selection with deltamethrin at F9 to evaluate the changes in allele and genotype frequencies. Our findings indicate that fitness costs were higher with the 410L+1016I+1534C allele, relative to the 1534C allele, in the absence of deltamethrin exposure, but that the 410L+1016I+1534C allele provides a stronger advantage when exposed to deltamethrin relative to the 1534C allele. Changes in genotype frequencies were not in Hardy-Weinberg equilibrium and could not be explained by drift. Our results suggest the diametrically opposed fitness costs in the presence and absence of insecticides is a reason for the variations in frequencies between the 410L+1016I+1534C and 1534C alleles in field populations.

A demo-genetic model shows how silviculture reduces natural density-dependent selection in tree populations.

Biological production systems and conservation programs benefit from and should care for evolutionary processes. Developing evolution-oriented strategies requires knowledge of the evolutionary consequences of management across timescales. Here, we used an individual-based demo-genetic modelling approach to study the interactions and feedback between tree thinning, genetic evolution, and forest stand dynamics. The model combines processes that jointly drive survival and mating success-tree growth, competition and regeneration-with genetic variation of quantitative traits related to these processes. In various management and disturbance scenarios, the evolutionary rates predicted by the coupled demo-genetic model for a growth-related trait, vigor, fit within the range of empirical estimates found in the literature for wild plant and animal populations. We used this model to simulate non-selective silviculture and disturbance scenarios over four generations of trees. We characterized and quantified the effect of thinning frequencies and intensities and length of the management cycle on viability selection driven by competition and fecundity selection. The thinning regimes had a drastic long-term effect on the evolutionary rate of vigor over generations, potentially reaching 84% reduction, depending on management intensity, cycle length and disturbance regime. The reduction of genetic variance by viability selection within each generation was driven by changes in genotypic frequencies rather than by gene diversity, resulting in low-long-term erosion of the variance across generations, despite short-term fluctuations within generations. The comparison among silviculture and disturbance scenarios was qualitatively robust to assumptions on the genetic architecture of the trait. Thus, the evolutionary consequences of management result from the interference between human interventions and natural evolutionary processes. Non-selective thinning, as considered here, reduces the intensity of natural selection, while selective thinning (on tree size or other criteria) might reduce or reinforce it depending on the forester's tree choice and thinning intensity.

Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population.

Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

Alu Deletions in LAMA2 and CDH4 Genes Are Key Components of Polygenic Predictors of Longevity.

Longevity is a unique human phenomenon and a highly stable trait, characterized by polygenicity. The longevity phenotype occurs due to the ability to successfully withstand the age-related genomic instability triggered by Alu elements. The purpose of our cross-sectional study was to evaluate the combined contribution of ACE*Ya5ACE, CDH4*Yb8NBC516, COL13A1*Ya5ac1986, HECW1*Ya5NBC182, LAMA2*Ya5-MLS19, PLAT*TPA25, PKHD1L1*Yb8AC702, SEMA6A*Yb8NBC597, STK38L*Ya5ac2145 and TEAD1*Ya5ac2013 Alu elements to longevity. The study group included 2054 unrelated individuals aged from 18 to 113 years who are ethnic Tatars from Russia. We analyzed the dynamics of the allele and genotype frequencies of the studied Alu polymorphic loci in the age groups of young (18-44 years old), middle-aged (45-59 years old), elderly (60-74 years old), old seniors (75-89 years old) and long-livers (90-113 years old). Most significant changes in allele and genotype frequencies were observed between the long-livers and other groups. The search for polygenic predictors of longevity was performed using the APSampler program. Attaining longevity was associated with the combinations LAMA2*ID + CDH4*D (OR = 2.23, PBonf = 1.90 × 10-2) and CDH4*DD + LAMA2*ID + HECW1*D (OR = 4.58, PBonf = 9.00 × 10-3) among persons aged between 18 and 89 years, LAMA2*ID + CDH4*D + SEMA6A*I for individuals below 75 years of age (OR = 3.13, PBonf = 2.00 × 10-2), LAMA2*ID + HECW1*I for elderly people aged 60 and older (OR = 3.13, PBonf = 2.00 × 10-2) and CDH4*DD + LAMA2*D + HECW1*D (OR = 4.21, PBonf = 2.60 × 10-2) and CDH4*DD + LAMA2*D + ACE*I (OR = 3.68, PBonf = 1.90 × 10-2) among old seniors (75-89 years old). The key elements of combinations associated with longevity were the deletion alleles of CDH4 and LAMA2 genes. Our results point to the significance for human longevity of the Alu polymorphic loci in CDH4, LAMA2, HECW1, SEMA6A and ACE genes, involved in the integration systems.

NOD1/CARD4(G796A) and NOD2/CARD15(R702W, G908R and L1007fsinC) polymorphisms associated with Crohn's disease in Iraqi patients

Inflammatory bowel disease (IBD) applies to two main forms of chronic relapsing inflammatory intestinal disorders: Crohn's disease (CD), Ulcerative colitis (UC). CD requires an irregular immune reaction that induces intense inflammation. The cause of CD disease is not yet fully known; previous research, however, indicated inflammation of the intestines elevated or continues due to inappropriate immune responses due to associations between genetic factors, intestinal microbiota, and environmental factors contributing to the production of IBD. This study aimed to investigate predisposing genes, single nucleotide Polymorphisms (SNPs) NOD1/CARD4 and NOD2/CARD15) with CD in Iraqi patients. The common NOD1 (G796A) SNP and NOD2 SNPs R702W, G908R and L1007fsinC for NOD2 SNPs were selected. Thirty Iraqi citizens with a recognized diagnosis of CD and twenty apparently healthy controls were included in the study from November 2019 to December 2020; the common NOD1 and NOD2 polymorphisms have been screened by the polymerase chain reaction/restriction analysis length polymorphism (PCR/RFLP). The results of the current investigation for NOD1 polymorphism in studied patients and controls, the allelic and genotypic data show a highly significant association of G796A SNPs in the NOD1 with Crohn's disease, GA percentage was 56.67% in patients as compared to controls genotype was (0.00%). Furthermore, the G allele was more common in Crohn's patients than the A allele 0.72 vs. 0.28. Also, the allelic and genotypic frequency distribution of the studied NOD2 SNPs in the current study were (R702W, G908R, and L1007fs) in Iraqi patients, and controls revealed a highly significant connection between the G908R SNP with Crohn's disease susceptibility. The proportion of the genotype GC was 30% in patients while 0% in the control group, the frequency of the G allele was 0.85 vs 0.15 respectively, which was more than the frequency of the A allele. There were no significant changes in genotypic and allelic frequencies of the R702W and L1007fs SNPs in Iraqi Crohn's disease patients. The present study concluded that the NOD1 SNP of allelic and genotypic data show a highly significant association of G796A with a predisposition to Crohn's disease in Iraqi patients. And the NOD2 SNPs of G908R were also revealed to be highly effective. While the other studied SNPs were R702W and L1007fsinsC of NOD2, which showed no significant changes in the allelic and genotypic frequencies of the SNPs with Crohn's disease Iraqi patients. Keywords: Inflammatory bowel disease, Crohn's disease, NOD1/CARD4, NOD2/CARD15, polymorphisms.

Change in prey genotype frequency rescues predator from extinction.

Indirect evolutionary rescue (IER) is a mechanism where a non-evolving species is saved from extinction in an otherwise lethal environment by evolution in an interacting species. This process has been described in a predator–prey model, where extinction of the predator is prevented by a shift in the frequency of defended towards undefended prey when reduced predator densities lower selection for defended prey. We test here how increased mortality and the initial frequencies of the prey types affect IER. Combining the analysis of model simulations and experiments with rotifers feeding on algae we show IER in the presence of increased predator mortality. We found that IER was dependent on the ability of the prey to evolve as well as on the frequency of the defended prey. High initial frequencies of defended prey resulted in predator extinction despite the possibility for prey evolution, as the increase in undefended prey was delayed too much to allow predator rescue. This frequency dependency for IER was more pronounced for higher predator mortalities. Our findings can help informing the development of conservation and management strategies that consider evolutionary responses in communities to environmental changes.

Bulk-Fitness Measurements Using Barcode Sequencing Analysis in Yeast.

The use of DNA barcodes for determining changes in genotype frequencies has been instrumental to increase the scale at which we can phenotype strain libraries by using next-generation sequencing technologies. Here, we describe the determination of strain fitness for thousands of yeast strains simultaneously in a single assay using recent innovations that increase the precision of these measurements, such as the inclusion of unique-molecular identifiers (UMIs) and purification by solid-phase reverse immobilization (SPRI) beads.

All resistance alleles are not equal: the high fitness cost of super-kdr in the absence of insecticide.

Mutations in the voltage-sensitive sodium channel are an important mechanism of resistance to pyrethroid insecticides. In Musca domestica, common resistance alleles are kdr, super-kdr and kdr-his. The levels of resistance that these alleles confer is known, but the fitness of these alleles relative to each other and to susceptible alleles is unknown. We used crosses from congenic strains of M.domestica to establish populations with known allele frequencies and then examined the changes in allele and genotype frequencies over 25 generations under laboratory conditions. There was a significant fitness cost for the super-kdr allele, which decreased from the starting frequency of 0.25 to 0.05 after 25 generations. The fitness of the kdr, kdr-his and susceptible alleles were similar. The greatest change in genotype frequency was seen for the super-kdr/super-kdr genotype, which was no longer detected after 25 generations. The fitness cost associated with the super-kdr allele is consistent with previous reports and appears to be a factor in helping to restrain high levels of resistance in field populations (the super-kdr allele confers higher levels of resistance than kdr or kdr-his). It is known that the relative costs of different alleles are environmentally dependent, but our results also demonstrate that the relative fitness of given alleles depends on which alleles are present in a given population, as previous pairwise comparisons of allele fitness do not exactly match (except for super-kdr) the results obtained using this four allele study. © 2020 Society of Chemical Industry.

Characterization of Sodium Channel Mutations in the Dengue Vector Mosquitoes Aedes aegypti and Aedes albopictus within the Context of Ongoing Wolbachia Releases in Kuala Lumpur, Malaysia.

Specific sodium channel gene mutations confer target site resistance to pyrethroid insecticides in mosquitoes and other insects. In Aedes mosquito species, multiple mutations that contribute to resistance vary in their importance around the world. Here, we characterize voltage sensitive sodium channel (Vssc) mutations in populations of Aedesaegypti from Kuala Lumpur, Malaysia, and look at their persistence in populations affected by ongoing Wolbachia releases (a dengue control measure). We also describe a Vssc mutation in Aedesalbopictus (F1534L) found for the first time in Malaysia. We show that there are three predominant Vssc haplotypes in Aedesaegypti in this region, which all persist with regular backcrossing, thereby maintaining the original genetic composition of the populations. We identify changes in genotype frequency in closed populations of Ae. aegypti maintained for multiple generations in laboratory culture, suggesting different fitness costs associated with the genotypes, some of which may be associated with the sex of the mosquito. Following population replacement of Ae. aegypti by Wolbachia in the target area, however, we find that the Vssc mutations have persisted at pre-release levels. Mosquitoes in two genotype classes demonstrate a type I pyrethroid resistance advantage over wildtype mosquitoes when exposed to 0.25% permethrin. This resistance advantage is even more pronounced with a type II pyrethroid, deltamethrin (0.03%). The results point to the importance of these mutations in pyrethroid resistance in mosquito populations and the need for regular backcrossing with male mosquitoes from the field to maintain similarity of genetic background and population integrity during Wolbachia releases.

Temporal changes in gene expression and genotype frequency of the ornithine decarboxylase gene in native silverside Basilichthys microlepidotus: Impact of wastewater reduction due to implementation of public policies.

Human activity has caused a deterioration in the health and population size of riverine species; thus, public policies have been implemented to mitigate the anthropogenic impacts of water use, watercourse transformation, and pollution. We studied the Maipo River Basin, one of the most polluted with untreated wastewater in Chile, for a period of 12 years (2007‐2019). Since the implementation of new public policies, including the operation of a wastewater collector (2012), the Maipo River Basin is currently much less polluted by untreated water than before. To analyze the impact of wastewater reduction in this river basin, we studied the native silverside (Basilichthys microlepidotus), which inhabits both polluted and unpolluted areas of the river basin. Previous studies reported the overexpression of the ornithine decarboxylase (odc) gene, heterozygote deficit, and high frequency of a homozygote odc genotype in silverside populations that inhabit wastewater‐polluted sites, suggesting a phenotypic change and genotypic selection in response to pollution. Here, a population affected and another population unaffected by wastewater were studied before and after implementing the wastewater collector. The physicochemical data of water samples, changes in odc expression and microsatellite variability, and odc genotype frequencies were analyzed. The results showed physicochemical changes in the affected site before and after the operation of the wastewater collector. The microsatellite loci showed no changes in either population. The odc expression in the affected site was higher before the operation of the wastewater collector. Significant changes in the genotype frequencies of the odc gene before and after the wastewater collector operation were detected only at the affected site, wherein the homozygous dominant genotype decreased from >59% to <25%. Our results suggest that public policies aimed at mitigating aquatic pollution can indirectly affect both gene expression and genotype frequencies of important functional genes.

Effects of balancing selection and microhabitat temperature variations on heat tolerance of the intertidal black mussel Septifer virgatus

Realistic assessments of the impacts of global warming on population extinction risk are likely to require an integrated analysis of the roles of standing genetic variation, microhabitat thermal complexity, and the inter-individual variation of heat tolerance due to both genetic differences and seasonal acclimatization effects. Here, we examine whether balancing selection and microhabitat temperature heterogeneity can interact to enhance the population persistence to thermal stress for the black mussel Septifer virgatus. We deployed biomimetic data loggers on the shore to measure the microhabitat-specific thermal variation from June 2014 to April 2016. Thermal tolerance of specimens was indexed by measuring effects of temperature on heart rate. Genotyping of specimens was performed using double digestion restriction association RADSeq (ddRADseq). Our results show that inter-individual variations in thermal tolerance correlate significantly with genetic differences at some specific gene loci, and that heterozygotes have higher thermal tolerances than homozygotes. The observed seasonal changes in genotype frequency suggest that these loci are under balancing selection. The ability of thermally resistant heterozygotes to survive in sun-exposed microhabitats acts to balance the loss of homozygotes during summer and enable the persistence of genetic polymorphisms. Population persistence of the mussel is also facilitated by the micro-scale variation in temperature, which provides refugia from thermal stress. Our results emphasize that inter-individual variation in thermal tolerance and in microhabitat heterogeneity in temperature are important for the persistence of populations in rocky shore habitats.

Evaluation of the relationship of IL17A and IL17F gene polymorphisms with the response to treatment in psoriatic patients using biological drugs: case-control study in patients in eastern Turkey

IntroductionIL-17A and IL-17F cytokines have important roles in the pathogenesis of psoriasis.AimTo examine the associations of IL-17A rs2275913 and IL-17F rs763780 variants with the development of psoriasis and whether these polymorphisms affect the responsiveness of biological agents.Material and methodsIn our case-controlled study, which included 83 psoriatic patients who were treated with different biological agents and 69 healthy controls, we genotyped IL-17A rs2275913 and IL-17F rs763780 variants using TaqMan probes.ResultsWe did not observe statistically significant changes in genotype frequencies of IL-17A rs2275913 (p = 0.922) and IL-17F rs763780 (p = 0.621) variants between patient and control groups. Although we did not find any association between these polymorphisms and the development of psoriasis, statistical analyses showed that individuals with the IL-17A AA genotype had shorter disease duration (9.09 ±6.82, p = 0.020) and AA genotype frequency was higher in patients who used single conventional treatment (34.6%; p = 0.025). IL17A/rs2275913 variant in terms of disease duration, it was observed that individuals with AA genotype had a shorter disease duration (less than 10 years) (p = 0.009). For patients with PASI90 and PASI100 response, the IL-17A AA genotype was significantly higher (p = 0.015). On the other hand, we did not detect any statistically significant correlation between variants and response to biological agents.ConclusionsAccording to our results, we may suggest that rs2275913 variant seems to be associated with disease duration, use of single conventional treatment and responsiveness of PASI90 and PASI100 however both variants have no effect on the susceptibility to psoriasis in the population of Eastern Turkey.

EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

BackgroundHigh throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data.ResultsHere we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data.ConclusionsEvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq.

Mitochondrial DNA Fitness Depends on Nuclear Genetic Background in Drosophila.

Mitochondrial DNA (mtDNA) has been one of the most extensively studied molecules in ecological, evolutionary and clinical genetics. In its early application in evolutionary genetics, mtDNA was assumed to be a selectively neutral marker conferring negligible fitness consequences for its host. However, this dogma has been overturned in recent years due to now extensive evidence for non-neutral evolutionary dynamics. Since mtDNA proteins physically interact with nuclear proteins to provide the mitochondrial machinery for aerobic ATP production, among other cell functions, co-variation of the respective genes is predicted to affect organismal fitness. To test this hypothesis we used an mtDNA-nuclear DNA introgression model in Drosophila melanogaster to test the fitness of genotypes in perturbation-reperturbation population cages and in a non-competitive assay for female fecundity. Genotypes consisted of both conspecific and heterospecific mtDNA-nDNA constructs, with either D. melanogaster or D. simulans mtDNAs on two alternative D. melanogaster nuclear backgrounds, to investigate mitonuclear genetic interactions (G x G effects). We found considerable variation between nuclear genetic backgrounds on the selection of mtDNA haplotypes. In addition, there was variation in the selection on mtDNAs pre- and post- reperturbation, demonstrating overall poor repeatability of selection. There was a strong influence of nuclear background on non-competitive fecundity across all the mtDNA species types. In only one of the four cage types did we see a significant fecundity effect between genotypes that could help explain the respective change in genotype frequency over generational time. We discuss these results in the context of G x G interactions and the possible influence of stochastic environments on mtDNA-nDNA selection.

Effect of temperature variation in Agarophyton chilensis: contrasting the response of natural and farmed populations

During the domestication process, farmers influence the reproduction and care of organisms to ensure a predictable supply of the resource of interest, causing changes in phenotypic and genotypic character frequencies. In Chile, as a result of unconscious selection and domestication process, farmed populations of the red alga Agarophyton chilensis have most likely undergone a reduction in genetic diversity and a modification in life-history traits compared to wild populations. In order to understand the implications that these processes may have in A. chilensis, we investigated how temperature variations (10 °C, 15 °C, and 20 °C) affect growth and photosynthetic responses of natural and farmed populations from three different localities along the Chilean coast. Natural population’s growth decreased at low and high temperature levels while all three farmed populations respond in a very similar way to temperature variation. We propose that a possible outcome of farming, in the A. chilensis, vegetatively propagated crops, could have been the selection of general-purpose-genotypes able to perform adequately across the range of temperature tested in our experiment. Furthermore, our results showed that photosynthetic activity was also affected by temperature treatments (e.g., different maximum maximal electron transport rate and quantum yield values depending on the population type and temperature). In a context of climate change, A. chilensis farmed populations may be better able to cope with impacts of anthropogenic activities than natural populations due to the buffer effect of their general-purpose-genotypes, tolerant to a wide range of conditions.

Changes in gene and genotype frequencies during the development of the grass carp Ctenopharyngodon idella.

In this study, a full-sib population of Ctenopharyngodon idella was constructed and approximately 500 C. idella individuals were sampled at four early developmental stages (hatching, first feeding, juvenile fish and young fish). Four DNA pools were constructed and subjected to next-generation sequencing. On the basis of the identification of single nucleotide polymorphisms (SNP), changes in gene and genotype frequencies during the developmental progress of C. idella were revealed, which indicates that death during the early developmental stage is not a random process. These findings will establish the basis for further studies performed for identifying superior alleles or genotypes as target markers for molecular breeding.

Evolution during population spread affects plant performance in stressful environments

Abstract Reliable predictions of population spread rates are essential to forecast biological invasions. Recent studies have shown that populations spreading through favourable habitat can rapidly evolve higher dispersal and reproductive rates at the expansion front, which accelerates spread velocity. However, spreading populations are likely to eventually encounter stressful conditions in the expanded range. How evolution during spread in favourable environments affects subsequent population growth in harsher environments is currently unknown. We examined evolutionary change in performance under drought, interspecific competition, and heat stress for populations of Arabidopsis thaliana that experienced six generations of spread through replicated experimental landscapes of favourable habitat. To quantify how population performance under stress differed between leading edge and founding populations, we combined individual tests of genotype performance under stress with knowledge of the genotype frequency changes that occurred over the replicate invasions. After spreading through favourable environments, the average silique production of individuals exposed to drought or interspecific competition was lower in leading edge than founding populations. This change was driven by the evolution of lower intrinsic silique production, which was correlated with increased seed size, a trait that evolved as populations spread. The ability of plants to tolerate drought or interspecific competition, however, did not change markedly during spread. Heat tolerance did increase in leading edge populations, and this trait was associated with the evolution of taller plants during spread through favourable habitat. Synthesis. We conclude that evolution during spread in favourable environments may affect the ability of populations to grow under stressful conditions as experienced in the expanded range, through changes in either intrinsic fecundity or stress tolerance. Thus, evolution during spread may constrain or extend the eventual range limit of nonnative species invasions.

Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya

BackgroundGlossina pallidipes is a major vector of both Human and Animal African Trypanosomiasis (HAT and AAT) in Kenya. The disease imposes economic burden on endemic regions in Kenya, including south-western Kenya, which has undergone intense but unsuccessful tsetse fly control measures. We genotyped 387 G. pallidipes flies at 13 microsatellite markers to evaluate levels of temporal genetic variation in two regions that have been subjected to intensive eradication campaigns from the 1960s to the 1980s. One of the regions, Nguruman Escarpment, has been subject to habitat alteration due to human activities, while the other, Ruma National Park, has not. In addition, Nguruman Escarpment is impacted by the movement of grazing animals into the area from neighboring regions during the drought season. We collected our samples from three geographically close sampling sites for each of the two regions. Samples were collected between the years 2003 and 2015, spanning ~96 tsetse fly generations.ResultsWe established that allelic richness averaged 3.49 and 3.63, and temporal Ne estimates averaged 594 in Nguruman Escarpment and 1120 in Ruma National Park. This suggests that genetic diversity is similar to what was found in previous studies of G. pallidipes in Uganda and Kenya, implying that we could not detect a reduction in genetic diversity following the extensive control efforts during the 1960s to the 1980s. However, we did find differences in temporal patterns of genetic variation between the two regions, indicated by clustering analysis, pairwise FST, and Fisher’s exact tests for changes in allele and genotype frequencies. In Nguruman Escarpment, findings indicated differentiation among samples collected in different years, and evidence of local genetic bottlenecks in two locations previous to 2003, and between 2009 and 2015. In contrast, there was no consistent evidence of differentiation among samples collected in different years, and no evidence of local genetic bottlenecks in Ruma National Park.ConclusionOur findings suggest that, despite extensive control measures especially between the 1960s and the 1980s, tsetse flies in these regions persist with levels of genetic diversity similar to that found in populations that did not experience extensive control measures. Our findings also indicate temporal genetic differentiation in Nguruman Escarpment detected at a scale of > 80 generations, and no similar temporal differentiation in Ruma National Park. The different level of temporal differentiation between the two regions indicates that genetic drift is stronger in Nugruman Escarpment, for as-yet unknown reasons, which may include differences in land management. This suggests land management may have an impact on G. pallidipes population genetics, and reinforces the importance of long term monitoring of vector populations in estimates of parameters needed to model and plan effective species-specific control measures.

Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms.

Evolutionary rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23 to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35, 37°C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23°C) and high-temperature (32°C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9°C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche.