Creating outbred and inbred populations of haplodiploid mites to measure adaptive responses in the lab

AbstractLaboratory studies are often criticized for not being representative of processes occurring in natural populations. This can be partially mitigated by using lab populations that capture large amounts of variation. Additionally, many studies addressing adaptation of organisms to their environment are done with laboratory populations, using quantitative genetics or experimental evolution methodologies. Such studies rely on populations that are either highly outbred or inbred. However, the methodology underlying the generation of such biological resources are usually not explicitly documented.Given their small size, short generation time, amenability to laboratory experimentation and knowledge of their ecological interactions, haplodiploid spider mites are becoming a widely used model organism. Here, we describe the creation of outbred populations of two species of spider mites, Tetranychus urticae and T. evansi, obtained by performing controlled crosses between individuals from field-collected populations. Subsequently, from the outbred population of T. evansi, we derived inbred lines, by performing several generations of sib-mating. These can be used to measure broad-sense heritability as well as correlations among traits. Finally, we outline an experimental evolution protocol that can be widely used in other systems. Sharing these biological resources with other laboratories and combining them with the available powerful genetic tools for T. urticae (and other species) will allow consistent and comparable studies that greatly contribute to our understanding of ecological and evolutionary processes.

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Male fertility thermal limits predict vulnerability to climate warming

Nature Communications ◽

10.1038/s41467-021-22546-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Belinda van Heerwaarden ◽

Carla M. Sgrò

Keyword(s):

Climate Warming ◽

Experimental Evolution ◽

Male Fertility ◽

Extinction Risk ◽

Conservation Strategies ◽

Tropical Species ◽

Adaptive Responses ◽

Widespread Species ◽

Thermal Limits ◽

Critical Thermal Limits

AbstractForecasting which species/ecosystems are most vulnerable to climate warming is essential to guide conservation strategies to minimize extinction. Tropical/mid-latitude species are predicted to be most at risk as they live close to their upper critical thermal limits (CTLs). However, these assessments assume that upper CTL estimates, such as CTmax, are accurate predictors of vulnerability and ignore the potential for evolution to ameliorate temperature increases. Here, we use experimental evolution to assess extinction risk and adaptation in tropical and widespread Drosophila species. We find tropical species succumb to extinction before widespread species. Male fertility thermal limits, which are much lower than CTmax, are better predictors of species’ current distributions and extinction in the laboratory. We find little evidence of adaptive responses to warming in any species. These results suggest that species are living closer to their upper thermal limits than currently presumed and evolution/plasticity are unlikely to rescue populations from extinction.

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Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila

10.1101/2021.12.21.473698 ◽

2021 ◽

Author(s):

Jason A Tarkington ◽

Hao Zhang ◽

Ricardo Azevedo ◽

Rebecca Zufall

Keyword(s):

Genetic Variation ◽

Experimental Evolution ◽

Evolutionary Biology ◽

Genetic Architecture ◽

Nuclear Division ◽

Tetrahymena Thermophila ◽

Laboratory Populations ◽

Evolutionary Success ◽

Sexual Progeny ◽

Open Question

Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional processes that may also generate substantial genetic variation in some populations and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. Tetrahymena thermophila is a ciliate with an unusual mechanism of nuclear division, called amitosis, which can generate genetic variation among the asexual descendants of a newly produced sexual progeny. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.

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Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice

The ISME Journal ◽

10.1038/s41396-020-0690-7 ◽

2020 ◽

Vol 14 (10) ◽

pp. 2367-2380

Author(s):

Meriem Belheouane ◽

Marie Vallier ◽

Aleksa Čepić ◽

Cecilia J. Chung ◽

Saleh Ibrahim ◽

...

Keyword(s):

Model Organism ◽

Rrna Gene ◽

Ancestral State ◽

Mus Musculus Domesticus ◽

Skin Microbiota ◽

Wild Mice ◽

Resistant Species ◽

Rare Biosphere ◽

Laboratory Populations ◽

In The Wild

Abstract The house mouse is a key model organism in skin research including host–microbiota interactions, yet little is known about the skin microbiota of free-living mice. It is similarly unclear how closely laboratory mice, which typically live under exceptionally hygienic conditions, resemble the ancestral state of microbial variation in the wild. In this study, we sampled an area spanning 270 km2 in south-west France and collected 203 wild Mus musculus domesticus. We profiled the ear skin microbiota on standing and active communities (DNA-based and RNA-based 16 rRNA gene sequencing, respectively), and compared multiple community aspects between wild-caught and laboratory-reared mice kept in distinct facilities. Compared to lab mice, we reveal the skin microbiota of wild mice on the one hand to be unique in their composition within the Staphylococcus genus, with a majority of sequences most closely matching known novobiocin-resistant species, and display evidence of a rare biosphere. On the other hand, despite drastic disparities between natural and laboratory environments, we find that shared taxa nonetheless make up the majority of the core skin microbiota of both wild- and laboratory skin communities, suggesting that mammalian skin is a highly specialized habitat capable of strong selection from available species pools. Finally, the influence of environmental factors suggests RNA-based profiling as a preferred method to reduce environmental noise.

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Genetic variation affecting heart rate in Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672399003924 ◽

1999 ◽

Vol 74 (2) ◽

pp. 121-128 ◽

Cited By ~ 12

Author(s):

J. ROBBINS ◽

R. AGGARWAL ◽

R. NICHOLS ◽

G. GIBSON

Keyword(s):

Heart Rate ◽

Drosophila Melanogaster ◽

Heart Function ◽

Susceptibility Gene ◽

Natural Populations ◽

Model Organism ◽

Genetic Dissection ◽

Wild Type ◽

Quantitative Genetic ◽

Wide Range

Heart rate in pre-pupae of Drosophila melanogaster is shown to vary over a wide range from 2·5 to 3·7 beats per second. Quantitative genetic analysis of a sample of 11 highly inbred lines indicates that approaching one-quarter of the total variance in natural populations can be attributed to genetic differences between flies. A hypomorphic allele of the potassium channel gene ether-a-gogo, which is homologous to a human long-QT syndrome susceptibility gene (HERG), has a heart rate at the low end of the wild-type range, but this effect can be suppressed in certain wild-type genetic backgrounds. This study provides a baseline for investigation of pharmacological and other physiological influences on heart rate in the model organism, and implies that quantitative genetic dissection will provide insight into the molecular basis for variation in normal and arrhythmic heart function.

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Microorgans in herbivorous two-spotted spider mites regulate ecological interactions with lima bean plant

Journal of Plant Interactions ◽

10.1080/17429145.2010.544912 ◽

2011 ◽

Vol 6 (2-3) ◽

pp. 161-161 ◽

Cited By ~ 1

Author(s):

Hirokazu Ueda ◽

Rika Ozawa ◽

Junji Takabayashi ◽

Massimo Maffei ◽

Kazuhiko Matsuda

Keyword(s):

Lima Bean ◽

Spider Mites ◽

Bean Plant ◽

Ecological Interactions

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Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster

10.1101/186882 ◽

2017 ◽

Author(s):

Emily L. Behrman ◽

Virginia M. Howick ◽

Martin Kapun ◽

Fabian Staubach ◽

Alan O. Bergland ◽

...

Keyword(s):

Immune Function ◽

Evolutionary Biology ◽

Bacterial Load ◽

Rapid Change ◽

Natural Populations ◽

Immune Defense ◽

Functional Responses ◽

Immune Genes ◽

Latitudinal Transect ◽

Outbred Populations

AbstractUnderstanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes in a range of taxa. Here, we use immune defense in natural populations of D. melanogaster to understand the rate of evolution in natural populations and the genetics underlying the rapid change. We probed the immune system using the natural pathogens Enterococcus faecalis and Providencia rettgeri to measure post-infection survival and bacterial load of wild D. melanogaster populations collected across seasonal time along a latitudinal transect on the eastern North America (Massachusetts, Pennsylvania, and Virginia). There are pronounced and repeatable changes in the immune response over approximately 10 generations between the spring and fall populations with a significant but less distinct difference among geographic locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles in Thioester-containing protein 3 (Tep3) have different functional responses to infection and that epistatic interactions among seasonal Tep3 and Drosomycin-like 6 (Dro6) alleles produce the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defense in natural populations.

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Novel CRISPR/Cas9 gene drive constructs inDrosophilareveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations

10.1101/112011 ◽

2017 ◽

Cited By ~ 9

Author(s):

Jackson Champer ◽

Riona Reeves ◽

Suh Yeon Oh ◽

Chen Liu ◽

Jingxian Liu ◽

...

Keyword(s):

Natural Populations ◽

Model Organism ◽

Mendelian Inheritance ◽

Pathogen Transmission ◽

Resistance Allele ◽

Gene Drive ◽

Vector Borne Diseases ◽

Evolution Of Resistance ◽

Resistance Rates ◽

Vector Capacity

ABSTRACTA functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity. CRISPR/Cas9 gene drive promises such a mechanism, which works by converting cells that are heterozygous for the drive construct into homozygotes, thereby enabling super-Mendelian inheritance. Though CRISPR gene drive activity has already been demonstrated, a key obstacle for current systems is their propensity to generate resistance alleles. In this study, we developed two CRISPR gene drive constructs based on thenanosandvasapromoters that allowed us to illuminate the different mechanisms by which resistance alleles are formed in the model organismDrosophila melanogaster.We observed resistance allele formation at high rates both prior to fertilization in the germline and post-fertilization in the embryo due to maternally deposited Cas9. Assessment of drive activity in genetically diverse backgrounds further revealed substantial differences in conversion efficiency and resistance rates. Our results demonstrate that the evolution of resistance will likely impose a severe limitation to the effectiveness of current CRISPR gene drive approaches, especially when applied to diverse natural populations.

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Larval densities of the protected Striped lychnis moth Shargacucullia lychnis (Lepidoptera: Noctuidae) in Buckinghamshire

10.1101/2021.11.25.470005 ◽

2021 ◽

Author(s):

Juliano Morimoto ◽

Lucy Kerr

Keyword(s):

Natural History ◽

Population Density ◽

Developmental Stages ◽

Larval Density ◽

Natural Populations ◽

Adaptive Responses ◽

Larval Population ◽

History Information ◽

The Uk ◽

Lepidoptera Noctuidae

Natural history information is essential for ecologically-relevant inferences about (adaptive) responses in organismal biology. Yet, natural history data can be difficult to obtain, particularly for the developmental stages of holometabolous insects. This gap can compromise our ability to design controlled experiments that provide useful understanding of insect responses to changing environments and precludes our ability to understand how natural populations may respond to unpredictable climatic changes in their natural environment. In this study, we collated data from previous reports from the Butterfly Conservation Upper Thames Branch on the larval population density of Shargacucullia lychnis (Lepidoptera: Noctuidae) in Buckinghamshire. In the UK, S. lychnis is a protected species, for which natural history information can be invaluable for its effective conservation. We report here that the natural range of larval densities observed for S. lychnis across locations and years is 0.001 to 6.417 larvae per spike. More importantly, S. lychnis larval density has overall declined from 1996 to 2020, which could support previous reports of a contraction in population range for this species. Overall, this study provides invaluable information about larval population density for an important protected Lepidopteran species of the UK.

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Environments with a high probability of incompatible crosses do not select for mate avoidance in spider mites

10.1101/395301 ◽

2018 ◽

Cited By ~ 2

Author(s):

Leonor R Rodrigues ◽

Flore Zélé ◽

Inês Santos ◽

Sara Magalhães

Keyword(s):

Genetic Variation ◽

Mate Choice ◽

Mixed Infection ◽

Host Species ◽

Experimental Evolution ◽

High Probability ◽

Spider Mite ◽

Cytoplasmic Incompatibility ◽

Spider Mites ◽

Infection Frequency

AbstractArthropods are often infected withWolbachiainducing cytoplasmic incompatibility (CI), whereby crosses between uninfected females and infected males yield unviable fertilized offspring. Although uninfected females benefit from avoiding mating withWolbachia-infected males, this behaviour is not present in all host species. Here we measured the prevalence of this behaviour across populations of the spider miteTetranychus urticae. Females from five populations originally fully infected withWolbachiashowed no preference, possibly because they did not face the choice between compatible and incompatible mates in their environment. Hence, to determine whether this behaviour could be selected in populations with intermediateWolbachiainfection frequency, we performed 15 generations of experimental evolution of spider-mite populations under i) fullWolbachiainfection, ii) no infection, or iii) mixed infection. In the latter selection regime, where uninfected females were exposed to infected and uninfected males at every generation, mating duration increased relative to the uninfected regime, suggesting the presence of genetic variation for mating traits. However, mate choice did not evolve. Together, these results show that CI-inducingWolbachiaalone does not necessarily lead to the evolution of pre-copulatory strategies in uninfected hosts, even at intermediate infection frequency.

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Highly parallel genomic selection response in replicated Drosophila melanogaster populations with reduced genetic variation

10.1101/2021.04.06.438598 ◽

2021 ◽

Author(s):

Claire Burny ◽

Viola Nolte ◽

Marlies Dolezal ◽

Christian Schl&oumltterer

Keyword(s):

Drosophila Melanogaster ◽

Experimental Evolution ◽

Selection Response ◽

Adaptive Responses ◽

Genetic Redundancy ◽

Powerful Approach ◽

Polygenic Adaptation ◽

Parallel Selection ◽

Sufficient Variation ◽

Genomic Regions

Many adaptive traits are polygenic and frequently more loci contributing to the phenotype than needed are segregating in populations to express a phenotypic optimum. Experimental evolution provides a powerful approach to study polygenic adaptation using replicated populations adapting to a new controlled environment. Since genetic redundancy often results in non-parallel selection responses among replicates, we propose a modified Evolve and Resequencing (E&R) design that maximizes the similarity among replicates. Rather than starting from many founders, we only use two inbred Drosophila melanogaster strains and expose them to a very extreme, hot temperature environment (29°C). After 20 generations, we detect many genomic regions with a strong, highly parallel selection response in 10 evolved replicates. The X chromosome has a more pronounced selection response than the autosomes, which may be attributed to dominance effects. Furthermore, we find that the median selection coefficient for all chromosomes is higher in our two-genotype experiment than in classic E&R studies. Since two random genomes harbor sufficient variation for adaptive responses, we propose that this approach is particularly well-suited for the analysis of polygenic adaptation.

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