scholarly journals Non-random associations of maternally transmitted symbionts in insects: The roles of drift versus co-transmission and selection

2018 ◽  
Author(s):  
Mathé-Hubert Hugo ◽  
Heidi Kaech ◽  
Corinne Hertaeg ◽  
Christoph Vorburger
Keyword(s):  
Acyrthosiphon Pisum ◽  
Field Survey ◽  
Maternal Transmission ◽  
Effective Population ◽  
Know How ◽  
Pea Aphids ◽  
Random Assortment ◽  
Population Sizes ◽  
Occurrence Patterns ◽  
Transmission Failures

AbstractVirtually all higher organisms form holobionts with associated microbiota. To understand the biology of holobionts we need to know how species assemble and interact. Controlled experiments are suited to study interactions between particular symbionts, but they can only inform about a tiny portion of the diversity within each species. Alternatively, interactions can be inferred from associations among symbionts in the field that are more or less frequent than expected under random assortment. However, random assortment may not be a valid null hypothesis for maternally transmitted symbionts in finite populations, where drift alone can result in associations. Here we report results from a European field survey of endosymbionts in the pea aphid (Acyrthosiphon pisum), and we develop a model to study the effect of drift on symbiont associations under different population sizes, considering varying rates of horizontal and maternal transmission. The model showed that even though horizontal transmissions and maternal transmission failures tend to randomise symbiont associations, drift can induce significant departures from random assortment, at least in moderate-sized populations. Based on these results, we carefully interpret our field survey and we re-visit the association between Spiroplasma and Wolbachia in Drosophila neotestacea reported by Jaenike et al. (2010). For this and for several significant associations between symbionts in European pea aphids we conclude that under reasonable assumptions of effective population size, they are indeed likely to be maintained by biased co-transmission or selection. Our study shows that formulating appropriate null expectations can strengthen the biological inference from co-occurrence patterns in the field.

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

Genetics ◽  
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.

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

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
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.

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

2018 ◽  
Vol 20 (2) ◽  
pp. 167-184 ◽  
Author(s):  
John Waldman ◽  
S. Elizabeth Alter ◽  
Douglas Peterson ◽  
Lorraine Maceda ◽  
Nirmal Roy ◽  
...  
Keyword(s):  
Atlantic Sturgeon ◽  
Effective Population ◽  
Population Sizes ◽  
Acipenser Oxyrinchus

scholarly journals The Genetic History of France

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.

scholarly journals Drop when the stakes are high: adaptive, flexible use of dropping behaviour by aphids

Behaviour ◽  
2021 ◽  
pp. 1-21
Author(s):  
Rosalind K. Humphreys ◽  
Graeme D. Ruxton ◽  
Alison J. Karley
Keyword(s):  
Host Plant ◽  
Acyrthosiphon Pisum ◽  
Adalia Bipunctata ◽  
Macrosiphum Euphorbiae ◽  
Herbivorous Insects ◽  
Chrysoperla Carnea ◽  
Pea Aphids ◽  
Potato Aphids ◽  
Antipredator Defence

Abstract For herbivorous insects, dropping from the host plant is a commonly-observed antipredator defence. The use of dropping compared to other behaviours and its timing in relation to contact with a predator was explored in both pea aphids (Acyrthosiphon pisum) and potato aphids (Macrosiphum euphorbiae). Pea aphids dropped more frequently in response to ladybird adults (Adalia bipunctata) than lacewing larvae (Chrysoperla carnea). Potato aphids mainly walked away or backed-up in response to both predator types; but they dropped more frequently relative to other non-walking defences when faced with ladybird adults. Contact with a predator was an important influencer of dropping for both species, and most drops occurred from adjacent to the predator. Dropping appears to be a defence adaptively deployed only when the risk of imminent predation is high; factors that increase dropping likelihood include presence of faster-foraging predators such as adult ladybirds, predator proximity, and contact between aphid and predator.

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

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).

SEASONAL ABUNDANCE OF THE PEA APHID, ACYRTHOSIPHON PISUM (HOMOPTERA: APHIDIDAE), IN MANITOBA FIELD PEAS

1986 ◽  
Vol 118 (6) ◽  
pp. 601-607 ◽  
Author(s):  
G.A. Maiteki ◽  
R.J. Lamb ◽  
S.T. Ali-Khan
Keyword(s):  
Pisum Sativum ◽  
Acyrthosiphon Pisum ◽  
Pea Aphid ◽  
Seasonal Abundance ◽  
Economic Threshold ◽  
Field Peas ◽  
Pea Aphids

AbstractPea aphids, Acyrthosiphon pisum (Harris), were sampled from 1980 to 1983 in field peas, Pisum sativum (L.), in Manitoba. Sweep and foliage samples were taken in commercial fields and plots. Aphids were found in late May or early June soon after the crop emerged, but populations were low throughout June. Populations increased in July, when the crop was flowering and producing pods, and peaked in the latter half of July or early August in 3 of the 4 years, when pods were maturing. Populations decreased rapidly after the peak, as the plants senesced. In 1980, a drought year, aphid densities were low and the populations peaked in the middle of August. From 1981 to 1983, densities exceeded the economic threshold in all commercial fields and all but one of the plots that were sampled.

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

Diversity ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 164 ◽  
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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