Keywords: Population genetics

Gene drives for the extinction of wild metapopulations

Jason W. Olejarz, Martin A. Nowak ,  Journal of Theoretical Biology,  2023.
Population-suppressing gene drives may be capable of extinguishing wild populations, with proposed applications in conservation, agriculture, and public health. However, unintended and potentially disastrous consequences of release of drive-engineered individuals are extremely ...
Keywords: , , , , , , , , ,

Routes of Introduction of Anopheles gambiae Into Remote Islands in the Indian Ocean

R. E. Ditter, M. Campos, M. W. Crepeau, J. Pinto, A. Toilibou, Y. Amina, Y. Lee, A. J. Cornel and G. C. Lanzaro,  ,  2023.
The malaria vector Anopheles gambiae s.s., is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern ...
Keywords: , , , , , , , , ,

Synthetic gene drives as an anthropogenic evolutionary force

A. D. Cutter,  Trends in Genetics,  2023.
Genetic drive represents a fundamental evolutionary force that can exact profound change to the genetic composition of populations by biasing allele transmission. Herein I propose that the use of synthetic homing gene drives, the human-mediated analog of endogenous genetic ...
Keywords: , , , , , , , , ,

Invasion and maintenance of meiotic drivers in populations of ascomycete fungi

I. Martinossi-Allibert, C. Veller, S. L. Ament-Velasquez, A. A. Vogan, C. Rueffler and H. Johannesson,  Evolution,  20. 2021.
Meiotic drivers (MDs) are selfish genetic elements that are able to become overrepresented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether an MD ...
Keywords: , , , , , , , , ,

Demographic feedbacks can hamper the spatial spread of a gene drive

L. Girardin and F. Débarre,  arXiv,  2021.
Our results indicate that taking into account the interplay between population dynamics and population genetics might actually be crucial, as it can effectively reverse the direction of the invasion and lead to failure. Our findings can be extended to other bistable systems, such ...
Keywords: , , , , , , , , ,

Selfing is the safest sex for Caenorhabditis tropicalis

L. M. Noble, J. Yuen, L. Stevens, N. D. Moya, R. Persaud, M. Moscatelli, J. L. Jackson, G. Zhang, R. Chitrakar, L. R. Baugh, C. Braendle, E. C. Andersen, H. S. Seidel and M. V. Rockman,  eLife,  10:e62587. 2021.
We generated a chromosomal-scale genome for C. tropicalis and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is ...
Keywords: , , , , , , , , ,

Genetic pest management and the background genetics of release strains

P. T. Leftwich, L. G. Spurgin, T. Harvey-Samuel, C. J. E. Thomas, L. C. Paladino, M. P. Edgington and L. Alphey,  Philosophical Transactions of the Royal Society B: Biological Sciences,  376:20190805. 2020.
We discuss issues around strain selection and the potential consequences of such introgression. We conclude that such introgression is probably harmless in almost all circumstances, and could, in theory, provide specific additional benefits to the release programme. We outline ...
Keywords: , , , , , , , , ,

Wolbachia strain wAlbB maintains high density and dengue inhibition following introduction into a field population of Aedes aegypti

N. A. Ahmad, M.-V. Mancini, T. H. Ant, J. Martinez, G. M. R. Kamarul, W. A. Nazni, A. A. Hoffmann and S. P. Sinkins,  Philosophical Transactions of the Royal Society B: Biological Sciences,  376:20190809. 2020.
Here, wAlbB-carrying Ae. aegypti collected from the field 20 months after the cessation of releases showed no reduction in Wolbachia density or tissue distribution changes compared to a wAlbB laboratory colony. The wAlbB strain continued to induce complete unidirectional ...
Keywords: , , , , , , , , ,

Embracing Dynamic Models for Gene Drive Management

A. J. Golnar, E. Ruell, A. L. Lloyd and K. M. Pepin,  Trends in Biotechnology,  2020.
We describe how quantitative tools can reduce risk uncertainty, streamline empirical research, guide risk management, and promote cross-sector collaboration throughout the process of gene drive technology development and implementation.
Keywords: , , , , , , , , ,

Invasion and maintenance of spore killers in populations of ascomycete fungi

I. Martinossi-Allibert, C. Veller, S. L. Ament-Velásquez, A. A. Vogan, C. Rueffler and H. Johannesson,  bioRxiv,  2020.04.06.026989. 2020.
We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here ...
Keywords: , , , , , , , , ,

Case Study 1: Olive Fruit Fly (Bactrocera oleae)

Merle Preu, Johannes L. Frieß, Broder Breckling and Winfried Schröder,  Gene Drives at Tipping Points,  2020.
The olive fruit fly Bactrocera oleae is a phytophagous insect associated to olive trees (Olea europaea, Oleaceae). Its larvae monophagously feed on olive fruits, the fly is therefore considered the most severe pest of olive cultivation causing tremendous economic losses. The ...
Keywords: , , , , , , , , ,

Experimental manipulation of selfish genetic elements links genes to microbial community function

S. D. Quistad, G. Doulcier and P. B. Rainey,  Philosophical Transactions of the Royal Society B-Biological Sciences,  375:12. 2020.
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent ...
Keywords: , , , , , , , , ,

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes

H. Schmidt, T. C. Collier, M. J. Hanemaaijer, P. D. Houston, Y. Lee and G. C. Lanzaro,  Nature Communications,  11. 2020.
ere we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that similar to 90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a ...
Keywords: , , , , , , , , ,

Population-level multiplexing: A promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus

M. P. Edgington, T. Harvey-Samuel and L. Alphey,  Evolutionary Applications,  10. 2020.
CRISPR-based gene drives bias inheritance in their favour by inducing double-stranded breaks (DSBs) at wild-type homologous loci and using the drive transgene as a repair template-converting drive heterozygotes into homozygotes. Recent studies have shown that alternate ...
Keywords: , , , , , , , , ,

Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events

H. Schmidt, Y. Lee, T. C. Collier, M. J. Hanemaaijer, O. D. Kirstein, A. Ouledi, M. Muleba, D. E. Norris, M. Slatkin, A. J. Cornel and G. C. Lanzaro,  Communications Biology,  2. 2019.
Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros.
Keywords: , , , , , , , , ,

A century of bias in genetics and evolution

L. D. Hurst,  Heredity,  123:33-44. 2019.
Mendel proposed that the heritable material is particulate and that transmission of alleles is unbiased. An assumption of unbiased transmission was necessary to show how variation can be preserved in the absence of selection, so overturning an early objection to Darwinism. In the ...
Keywords: , , , , , , , , ,

Gene-drive-mediated extinction is thwarted by population structure and evolution of sib mating

J. J. Bull, C. H. Remien and S. M. Krone,  Evolution Medicine and Public Health,  2019:66-81. 2019.
Genetic engineering combined with CRISPR technology has developed to the point that gene drives can, in theory, be engineered to cause extinction in countless species. Success of extinction programs now rests on the possibility of resistance evolution, which is largely unknown. ...
Keywords: , , , , , , , , ,

Modeling the mutation and reversal of engineered underdominance gene drives

Edgington, MPA, Luke S.,  Journal of Theoretical Biology,  479:14-21. 2019.
A range of gene drive systems have been proposed that are predicted to increase their frequency and that of associated desirable genetic material even if they confer a fitness cost on individuals carrying them. Engineered underdominance (UD) is such a system and, in one version, ...
Keywords: , , , , , , , , ,

Ecological effects on underdominance threshold drives for vector control

D. Khamis, C. El Mouden, K. Kura and M. B. Bonsall,  Journal of Theoretical Biology,  456:1-15. 2018.
Here, ecological and epidemiological dynamics are coupled to a model of mosquito genetics to investigate theoretically the impact of different types of underdominance gene drive on disease prevalence. We model systems with two engineered alleles carried either on the same pair ...
Keywords: , , , , , , , , ,

Multiple loci of small effect confer wide variability in efficiency and resistance rate of CRISPR gene drive

J. Champer, Z. Wen, A. Luthra, R. Reeves, J. Chung, C. Liu, Y. L. Lee, J. Liu, E. Yang, P. W. Messer and A. G. Clark,  bioRxiv,  447615. 2018.
Gene drives could allow for control of vector-borne diseases by directly suppressing vector populations or spreading genetic payloads designed to reduce pathogen transmission. CRISPR homing gene drives work by cleaving wild-type alleles, which are then converted to drive alleles ...
Keywords: , , , , , , , , ,

Keywords: Population genetics

Gene drives for the extinction of wild metapopulations

Jason W. Olejarz, Martin A. Nowak ,  Journal of Theoretical Biology,  2023.
Population-suppressing gene drives may be capable of extinguishing wild populations, with proposed applications in conservation, agriculture, and public health. However, unintended and potentially disastrous consequences of release of drive-engineered individuals are extremely ...
Keywords: , , , , , , , , ,

Routes of Introduction of Anopheles gambiae Into Remote Islands in the Indian Ocean

R. E. Ditter, M. Campos, M. W. Crepeau, J. Pinto, A. Toilibou, Y. Amina, Y. Lee, A. J. Cornel and G. C. Lanzaro,  ,  2023.
The malaria vector Anopheles gambiae s.s., is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern ...
Keywords: , , , , , , , , ,

Synthetic gene drives as an anthropogenic evolutionary force

A. D. Cutter,  Trends in Genetics,  2023.
Genetic drive represents a fundamental evolutionary force that can exact profound change to the genetic composition of populations by biasing allele transmission. Herein I propose that the use of synthetic homing gene drives, the human-mediated analog of endogenous genetic ...
Keywords: , , , , , , , , ,

Invasion and maintenance of meiotic drivers in populations of ascomycete fungi

I. Martinossi-Allibert, C. Veller, S. L. Ament-Velasquez, A. A. Vogan, C. Rueffler and H. Johannesson,  Evolution,  20. 2021.
Meiotic drivers (MDs) are selfish genetic elements that are able to become overrepresented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether an MD ...
Keywords: , , , , , , , , ,

Demographic feedbacks can hamper the spatial spread of a gene drive

L. Girardin and F. Débarre,  arXiv,  2021.
Our results indicate that taking into account the interplay between population dynamics and population genetics might actually be crucial, as it can effectively reverse the direction of the invasion and lead to failure. Our findings can be extended to other bistable systems, such ...
Keywords: , , , , , , , , ,

Selfing is the safest sex for Caenorhabditis tropicalis

L. M. Noble, J. Yuen, L. Stevens, N. D. Moya, R. Persaud, M. Moscatelli, J. L. Jackson, G. Zhang, R. Chitrakar, L. R. Baugh, C. Braendle, E. C. Andersen, H. S. Seidel and M. V. Rockman,  eLife,  10:e62587. 2021.
We generated a chromosomal-scale genome for C. tropicalis and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is ...
Keywords: , , , , , , , , ,

Genetic pest management and the background genetics of release strains

P. T. Leftwich, L. G. Spurgin, T. Harvey-Samuel, C. J. E. Thomas, L. C. Paladino, M. P. Edgington and L. Alphey,  Philosophical Transactions of the Royal Society B: Biological Sciences,  376:20190805. 2020.
We discuss issues around strain selection and the potential consequences of such introgression. We conclude that such introgression is probably harmless in almost all circumstances, and could, in theory, provide specific additional benefits to the release programme. We outline ...
Keywords: , , , , , , , , ,

Wolbachia strain wAlbB maintains high density and dengue inhibition following introduction into a field population of Aedes aegypti

N. A. Ahmad, M.-V. Mancini, T. H. Ant, J. Martinez, G. M. R. Kamarul, W. A. Nazni, A. A. Hoffmann and S. P. Sinkins,  Philosophical Transactions of the Royal Society B: Biological Sciences,  376:20190809. 2020.
Here, wAlbB-carrying Ae. aegypti collected from the field 20 months after the cessation of releases showed no reduction in Wolbachia density or tissue distribution changes compared to a wAlbB laboratory colony. The wAlbB strain continued to induce complete unidirectional ...
Keywords: , , , , , , , , ,

Embracing Dynamic Models for Gene Drive Management

A. J. Golnar, E. Ruell, A. L. Lloyd and K. M. Pepin,  Trends in Biotechnology,  2020.
We describe how quantitative tools can reduce risk uncertainty, streamline empirical research, guide risk management, and promote cross-sector collaboration throughout the process of gene drive technology development and implementation.
Keywords: , , , , , , , , ,

Invasion and maintenance of spore killers in populations of ascomycete fungi

I. Martinossi-Allibert, C. Veller, S. L. Ament-Velásquez, A. A. Vogan, C. Rueffler and H. Johannesson,  bioRxiv,  2020.04.06.026989. 2020.
We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here ...
Keywords: , , , , , , , , ,

Case Study 1: Olive Fruit Fly (Bactrocera oleae)

Merle Preu, Johannes L. Frieß, Broder Breckling and Winfried Schröder,  Gene Drives at Tipping Points,  2020.
The olive fruit fly Bactrocera oleae is a phytophagous insect associated to olive trees (Olea europaea, Oleaceae). Its larvae monophagously feed on olive fruits, the fly is therefore considered the most severe pest of olive cultivation causing tremendous economic losses. The ...
Keywords: , , , , , , , , ,

Experimental manipulation of selfish genetic elements links genes to microbial community function

S. D. Quistad, G. Doulcier and P. B. Rainey,  Philosophical Transactions of the Royal Society B-Biological Sciences,  375:12. 2020.
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent ...
Keywords: , , , , , , , , ,

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes

H. Schmidt, T. C. Collier, M. J. Hanemaaijer, P. D. Houston, Y. Lee and G. C. Lanzaro,  Nature Communications,  11. 2020.
ere we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that similar to 90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a ...
Keywords: , , , , , , , , ,

Population-level multiplexing: A promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus

M. P. Edgington, T. Harvey-Samuel and L. Alphey,  Evolutionary Applications,  10. 2020.
CRISPR-based gene drives bias inheritance in their favour by inducing double-stranded breaks (DSBs) at wild-type homologous loci and using the drive transgene as a repair template-converting drive heterozygotes into homozygotes. Recent studies have shown that alternate ...
Keywords: , , , , , , , , ,

Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events

H. Schmidt, Y. Lee, T. C. Collier, M. J. Hanemaaijer, O. D. Kirstein, A. Ouledi, M. Muleba, D. E. Norris, M. Slatkin, A. J. Cornel and G. C. Lanzaro,  Communications Biology,  2. 2019.
Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros.
Keywords: , , , , , , , , ,

A century of bias in genetics and evolution

L. D. Hurst,  Heredity,  123:33-44. 2019.
Mendel proposed that the heritable material is particulate and that transmission of alleles is unbiased. An assumption of unbiased transmission was necessary to show how variation can be preserved in the absence of selection, so overturning an early objection to Darwinism. In the ...
Keywords: , , , , , , , , ,

Gene-drive-mediated extinction is thwarted by population structure and evolution of sib mating

J. J. Bull, C. H. Remien and S. M. Krone,  Evolution Medicine and Public Health,  2019:66-81. 2019.
Genetic engineering combined with CRISPR technology has developed to the point that gene drives can, in theory, be engineered to cause extinction in countless species. Success of extinction programs now rests on the possibility of resistance evolution, which is largely unknown. ...
Keywords: , , , , , , , , ,

Modeling the mutation and reversal of engineered underdominance gene drives

Edgington, MPA, Luke S.,  Journal of Theoretical Biology,  479:14-21. 2019.
A range of gene drive systems have been proposed that are predicted to increase their frequency and that of associated desirable genetic material even if they confer a fitness cost on individuals carrying them. Engineered underdominance (UD) is such a system and, in one version, ...
Keywords: , , , , , , , , ,

Ecological effects on underdominance threshold drives for vector control

D. Khamis, C. El Mouden, K. Kura and M. B. Bonsall,  Journal of Theoretical Biology,  456:1-15. 2018.
Here, ecological and epidemiological dynamics are coupled to a model of mosquito genetics to investigate theoretically the impact of different types of underdominance gene drive on disease prevalence. We model systems with two engineered alleles carried either on the same pair ...
Keywords: , , , , , , , , ,

Multiple loci of small effect confer wide variability in efficiency and resistance rate of CRISPR gene drive

J. Champer, Z. Wen, A. Luthra, R. Reeves, J. Chung, C. Liu, Y. L. Lee, J. Liu, E. Yang, P. W. Messer and A. G. Clark,  bioRxiv,  447615. 2018.
Gene drives could allow for control of vector-borne diseases by directly suppressing vector populations or spreading genetic payloads designed to reduce pathogen transmission. CRISPR homing gene drives work by cleaving wild-type alleles, which are then converted to drive alleles ...
Keywords: , , , , , , , , ,