Effective population sizes of a major vector of human diseases,Aedes aegypti

AbstractModified Aedes aegypti mosquitoes reared in laboratories are being released around the world to control wild mosquito populations and the diseases they transmit. Several efforts have failed due to poor competitiveness of the released mosquitoes. We hypothesized that colonized mosquito populations could suffer from inbreeding depression and adapt to laboratory conditions, reducing their performance in the field. We established replicate populations of Ae. aegypti mosquitoes collected from Queensland, Australia, and maintained them in the laboratory for twelve generations at different census sizes. Mosquito colonies maintained at small census sizes (≤100 individuals) suffered from inbreeding depression due to low effective population sizes which were only 25% of the census size as estimated by SNP markers. Populations that underwent full-sib mating for 9 consecutive generations had greatly reduced performance across all traits measured. We compared the established laboratory populations with their ancestral population resurrected from quiescent eggs for evidence of laboratory adaptation. The overall performance of laboratory populations maintained at a large census size (400 individuals) increased, potentially reflecting adaptation to artificial rearing conditions. However most individual traits were unaffected, and patterns of adaptation were not consistent across populations. Differences between replicate populations may indicate that founder effects and drift affect experimental outcomes. Though we find limited evidence of laboratory adaptation, mosquitoes maintained at low population sizes can clearly suffer fitness costs, compromising the success of “rear and release” strategies for arbovirus control.

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Faculty Opinions recommendation of Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.723874420.793504625 ◽

2015 ◽

Author(s):

Charles Baer

Keyword(s):

Caenorhabditis Elegans ◽

Spontaneous Mutation ◽

Mutation Accumulation ◽

Effective Population ◽

Population Sizes

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EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽

10.1093/genetics/73.3.513 ◽

1973 ◽

Vol 73 (3) ◽

pp. 513-530

Author(s):

J P Hanrahan ◽

E J Eisen ◽

J E Legates

Keyword(s):

Population Size ◽

Selection Response ◽

Selection Intensity ◽

Realized Heritability ◽

Family Selection ◽

Effective Population ◽

Population Sizes ◽

Selection For ◽

Selection Intensities ◽

Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

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The effect of life-history and mode of inheritance on neutral genetic variability

Genetics Research ◽

10.1017/s0016672301004979 ◽

2001 ◽

Vol 77 (2) ◽

pp. 153-166 ◽

Cited By ~ 114

Author(s):

BRIAN CHARLESWORTH

Keyword(s):

Sequence Variation ◽

Adult Mortality ◽

Structured Populations ◽

Human Populations ◽

Effective Population ◽

Transmission Modes ◽

Population Sizes ◽

Age Structured ◽

Infinite Sites Model ◽

Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

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Contemporary and historical effective population sizes of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus

Conservation Genetics ◽

10.1007/s10592-018-1121-4 ◽

2018 ◽

Vol 20 (2) ◽

pp. 167-184 ◽

Cited By ~ 1

Author(s):

John Waldman ◽

S. Elizabeth Alter ◽

Douglas Peterson ◽

Lorraine Maceda ◽

Nirmal Roy ◽

...

Keyword(s):

Atlantic Sturgeon ◽

Effective Population ◽

Population Sizes ◽

Acipenser Oxyrinchus

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The Genetic History of France

10.1101/712497 ◽

2019 ◽

Author(s):

Aude Saint Pierre ◽

Joanna Giemza ◽

Matilde Karakachoff ◽

Isabel Alves ◽

Philippe Amouyel ◽

...

Keyword(s):

Genetic Structure ◽

Demographic History ◽

Migration Routes ◽

Effective Population ◽

Genetic Studies ◽

Independent Population ◽

Genome Wide Data ◽

Population Sizes ◽

History Of ◽

Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

10.7287/peerj.preprints.314 ◽

2014 ◽

Author(s):

Jonathan Puritz ◽

Christopher M. Hollenbeck ◽

John R. Gold

Keyword(s):

Population Genomics ◽

De Novo ◽

Variant Calling ◽

Population Level ◽

Model Organisms ◽

Effective Population ◽

Reduction Techniques ◽

Indel Polymorphisms ◽

Indel Calling ◽

Population Sizes

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genetic polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is most likely due to the fact that dDocent quality trims instead of filtering and incorporates both forward and reverse reads in assembly, mapping, and SNP calling, thus enabling use of reads with Indel polymorphisms. The pipeline and a comprehensive user guide can be found at (http://dDocent.wordpress.com).

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Smaller effective population sizes evidenced by loss of microsatellite alleles in tributary-spawning populations of sockeye salmon from the Kvichak River, Alaska drainage

Genetics of Subpolar Fish and Invertebrates - Developments in environmental biology of fishes ◽

10.1007/978-94-007-0983-6_5 ◽

2004 ◽

pp. 51-62

Author(s):

Christopher Habicht ◽

Jeffrey B. Olsen ◽

Lowell Fair ◽

James E. Seeb

Keyword(s):

Sockeye Salmon ◽

Effective Population ◽

Population Sizes ◽

Microsatellite Alleles

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Deep-Time Demographic Inference Suggests Ecological Release as Driver of Neoavian Adaptive Radiation

Diversity ◽

10.3390/d12040164 ◽

2020 ◽

Vol 12 (4) ◽

pp. 164 ◽

Cited By ~ 2

Author(s):

Peter Houde ◽

Edward L. Braun ◽

Lawrence Zhou

Keyword(s):

Evolutionary Biology ◽

Gene Tree ◽

Difficult Problem ◽

Gene Trees ◽

Effective Population ◽

Deep Time ◽

Ecological Release ◽

Population Sizes ◽

Demographic Inference ◽

Gene Tree Discordance

Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction.

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Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2613 ◽

2020 ◽

Vol 287 (1922) ◽

pp. 20192613 ◽

Cited By ~ 2

Author(s):

Elisa G. Dierickx ◽

Simon Yung Wa Sin ◽

H. Pieter J. van Veelen ◽

M. de L. Brooke ◽

Yang Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Sex Chromosomes ◽

Demographic History ◽

Large Population ◽

Effective Population ◽

Island Species ◽

Population Sizes ◽

Approaches To Study ◽

Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

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