scholarly journals Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont

2016 ◽  
Vol 3 (5) ◽  
pp. 160130 ◽  
Author(s):  
Tetsuro Ikuta ◽  
Kanae Igawa ◽  
Akihiro Tame ◽  
Tsuneyoshi Kuroiwa ◽  
Haruko Kuroiwa ◽  
...  
Keyword(s):  
Population Size ◽  
Genetic Drift ◽  
Deep Sea ◽  
Small Population ◽  
Symbiotic Associations ◽  
Complex Interactions ◽  
Vegetal Pole ◽  
New Type ◽  
Symbiont Transmission ◽  
Sulfur Oxidizing

Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.

scholarly journals Demographic decline and lineage-specific adaptations characterize New Zealand kiwi

2021 ◽  
Vol 288 (1965) ◽  
Author(s):  
Jordan B. Bemmels ◽  
Else K. Mikkelsen ◽  
Oliver Haddrath ◽  
Rogan M. Colbourne ◽  
Hugh A. Robertson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Size ◽  
Genetic Drift ◽  
Demographic History ◽  
Small Population ◽  
Population Declines ◽  
Demographic Stochasticity ◽  
Fragmented Populations ◽  
Low Genetic Diversity

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

scholarly journals Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon

2020 ◽  
Author(s):  
Jiahao Gu ◽  
Xiaojun Wang ◽  
Xiaopan Ma ◽  
Ying Sun ◽  
Xiang Xiao ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Size ◽  
Mutation Rate ◽  
Genetic Drift ◽  
Deep Sea ◽  
High Mutation Rate ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Free Living

AbstractDeep-sea hydrothermal vents resemble the early Earth, and thus the dominant Thermococcaceae inhabitants, which occupy an evolutionarily basal position of the archaeal tree and take an obligate anaerobic hyperthermophilic free-living lifestyle, are likely excellent models to study the evolution of early life. Here, we determined that unbiased mutation rate of a representative species, Thermococcus eurythermalis, exceeded that of all known free-living prokaryotes by 1-2 orders of magnitude, and thus rejected the long-standing hypothesis that low mutation rates were selectively favored in hyperthermophiles. We further sequenced multiple and diverse isolates of this species and calculated that T. eurythermalis has a lower effective population size than other free-living prokaryotes by 1-2 orders of magnitude. These data collectively indicate that the high mutation rate of this species is not selectively favored but instead driven by random genetic drift. The availability of these unusual data also helps explore mechanisms underlying microbial genome size evolution. We showed that genome size is negatively correlated with mutation rate and positively correlated with effective population size across 30 bacterial and archaeal lineages, suggesting that increased mutation rate and random genetic drift are likely two important mechanisms driving microbial genome reduction. Future determinations of the unbiased mutation rate of more representative lineages with highly reduced genomes such as Prochlorococcus and Pelagibacterales that dominate marine microbial communities are essential to test these hypotheses.

Evolutionary genetics of small populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Evolutionary Genetic ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

Genetic and Nongenetic Bases for the L-Shaped Distribution of Quantitative Trait Loci Effects

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1773-1787 ◽  
Author(s):  
Bruno Bost ◽  
Dominique de Vienne ◽  
Frédéric Hospital ◽  
Laurence Moreau ◽  
Christine Dillmann
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Population Size ◽  
Quantitative Trait ◽  
Metabolic Flux ◽  
Genetic Model ◽  
Small Population ◽  
Additive Genetic Model ◽  
Metabolic Mechanism ◽  
Qtl Effects

Abstract The L-Shaped distribution of estimated QTL effects (R2) has long been reported. We recently showed that a metabolic mechanism could account for this phenomenon. But other nonexclusive genetic or nongenetic causes may contribute to generate such a distribution. Using analysis and simulations of an additive genetic model, we show that linkage disequilibrium between QTL, low heritability, and small population size may also be involved, regardless of the gene effect distribution. In addition, a comparison of the additive and metabolic genetic models revealed that estimates of the QTL effects for traits proportional to metabolic flux are far less robust than for additive traits. However, in both models the highest R2's repeatedly correspond to the same set of QTL.

scholarly journals Population Density or Populations Size. Which Factor Determines Urban Traffic Congestion?

2021 ◽  
Vol 13 (8) ◽  
pp. 4280
Author(s):  
Yu Sang Chang ◽  
Sung Jun Jo ◽  
Yoo-Taek Lee ◽  
Yoonji Lee
Keyword(s):  
Population Density ◽  
Population Size ◽  
Traffic Congestion ◽  
Critical Role ◽  
Small Population ◽  
High Density ◽  
Urban Traffic ◽  
Contradictory Result ◽  
Low Density

A large number of articles have documented that as population density of cities increases, car use declines and public transit use rises. These articles had a significant impact of promoting high-density compact urban development to mitigate traffic congestion. Another approach followed by other researchers used the urban scaling model to indicate that traffic congestion increases as population size of cities increases, thus generating a possible contradictory result. Therefore, this study examines the role of both density and population size on traffic congestion in 164 global cities by the use of Stochastic Impacts by Regression on Population, Affluence and Technology model. We divide 164 cities into the two subgroups of 66 low density cities and 98 high density cities for analysis. The findings from the subgroups analysis indicated a clear-cut difference on the critical role of density in low-density cities and the exclusive role of population size in high-density cities. Furthermore, using threshold regression model, 164 cities are divided into the two regions of large and small population cities to determine population scale advantage of traffic congestion. Our findings highlight the importance of including analysis of subgroups based on density and/or population size in future studies of traffic congestion.

Eumops floridanus (Chiroptera: Molossidae)

2021 ◽  
Vol 53 (1009) ◽  
pp. 125-133
Author(s):  
Jessica M Vannatta ◽  
Jeffery A Gore ◽  
Verity L Mathis ◽  
Brian D Carver
Keyword(s):  
United States ◽  
Population Size ◽  
The United States ◽  
Small Population ◽  
Species Level ◽  
Small Population Size ◽  
Restricted Distribution ◽  
Dead Trees ◽  
Fish And Wildlife Service

Abstract Eumops floridanus (Allen, 1932) is a molossid commonly called the Florida bonneted bat or the Florida mastiff bat. Eumops floridanus is the largest species of bat in Florida and is one of 16 species in the genus Eumops. With one of the smallest distributions of any bat in the United States, it is endemic to southern peninsular Florida where it roosts in cavities of live and dead trees and man-made structures. Eumops floridanus was formerly classified as a subspecies of E. glaucinus but has been elevated to species level based on morphology. Due primarily to its restricted distribution, small population size, and the continued loss of habitat, E. floridanus is federally listed as “Endangered” (EN) by the United States Fish and Wildlife Service.

scholarly journals Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size

PLoS ONE ◽  
2018 ◽  
Vol 13 (6) ◽  
pp. e0198901 ◽  
Author(s):  
Nicole L. Crane ◽  
Juliette Tariel ◽  
Jennifer E. Caselle ◽  
Alan M. Friedlander ◽  
D. Ross Robertson ◽  
...  
Keyword(s):  
Population Size ◽  
Small Population ◽  
Small Population Size

scholarly journals Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model

2020 ◽  
Author(s):  
Enikő Szép ◽  
Himani Sachdeva ◽  
Nick Barton
Keyword(s):  
Population Size ◽  
Local Adaptation ◽  
Genetic Drift ◽  
Diffusion Approximation ◽  
Joint Distribution ◽  
Evolutionary Model ◽  
Ecological Niches ◽  
Demographic Stochasticity ◽  
Linkage Disequilibria ◽  
Population Sizes

AbstractThis paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.

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