Strong neutral sweeps occurring during a population contraction

A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to similar reduction in local diversity, especially when the population experiences changes in population size, e.g., bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such neutral sweeps and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. We apply our framework to the case of a putative selective sweep signal around the gene Quetzalcoatl in D. melanogaster and show that the valley of diversity in the vicinity of this gene is compatible with a short bottleneck scenario without selection. Our findings provide further insight in how simple demographic models can create valleys of genetic diversity that may falsely be attributed to positive selection.

Download Full-text

Palliating the impact of fixation of a major gene on the genetic variation of artificially selected polygenes

Genetics Research ◽

10.1017/s0016672306008421 ◽

2006 ◽

Vol 88 (2) ◽

pp. 105-118 ◽

Cited By ~ 5

Author(s):

LEOPOLDO SÁNCHEZ ◽

ARMANDO CABALLERO ◽

ENRIQUE SANTIAGO

Keyword(s):

Population Size ◽

Effective Population Size ◽

Selective Sweep ◽

Major Gene ◽

Optimal Path ◽

Fixation Time ◽

Selection Intensity ◽

Effective Population ◽

The Impact ◽

Polygenic Variation

Selective sweeps of variation caused by fixation of major genes may have a dramatic impact on the genetic gain from background polygenic variation, particularly in the genome regions closely linked to the major gene. The response to selection can be restrained because of the reduced selection intensity and the reduced effective population size caused by the increase in frequency of the major gene. In the context of a selected population where fixation of a known major gene is desired, the question arises as to which is the optimal path of increase in frequency of the gene so that the selective sweep of variation resulting from its fixation is minimized. Using basic theoretical arguments we propose a frequency path that maximizes simultaneously the effective population size applicable to the selected background and the selection intensity on the polygenic variation by minimizing the average squared selection intensity on the major gene over generations up to a given fixation time. We also propose the use of mating between carriers and non-carriers of the major gene, in order to promote the effective recombination between the major gene and its linked polygenic background. Using a locus-based computer simulation assuming different degrees of linkage, we show that the path proposed is more effective than a similar path recently published, and that the combination of the selection and mating methods provides an efficient way to palliate the negative effects of a selective sweep.

Download Full-text

POPULATION SIZE CHANGE IN RURAL AREAS OF WEST POMERANIAN VOIVODESHIP IN 2011–2014

Journal of Agribusiness and Rural Development ◽

10.17306/j.jard.2018.00393 ◽

2018 ◽

Vol 47 (1) ◽

pp. 65-72

Author(s):

Luiza Ossowska ◽

Natalia Bartkowiak-Bakun

Keyword(s):

Growth Rate ◽

Population Size ◽

Rural Areas ◽

Population Growth Rate ◽

Local Level ◽

Natural Increase ◽

Demographic Information ◽

Size Change ◽

Net Migration ◽

Population Size Change

The aim of this study is to discuss changes in thepopulation and indicate the main reasons of these changes inrural areas of West Pomeranian voivodeship. The study wasconducted on the local level and based on Central StatisticalOffice data from the years 2010 to 2014. In the first part ofthe research, main demographic information is discussed. Itincludes population density, natural increase per 1000 populationand net migration per 1000 population in rural areasof West Pomeranian voivodeship. In the next part of the research,the average population growth rate was counted in theyears 2011–2014. Based on these changes, researched unitswere divided into four groups – two groups with positivechanges and two groups with negative changes. Subsequently,the main reasons of the changes in population size were analyzedin particular groups including natural increase, migration,population structure by age, level of unemployment andentrepreneurship. All indicators were designated as averagesfrom 2011 to 2014. According to the results in most of the researchunits, the net migration determined the population size.The net migration was characterized by higher absolute valuesthan natural increase. The population size changes are relatedto density. The lowest density areas are more depopulated.Moreover, the population size changes are positive related tothe level of entrepreneurship and negative related to the levelof unemployment.

Download Full-text

Contrasting Trends of Population Size Change for Two Eurasian Owlet Species—Athene brama and Glaucidium radiatum From South Asia Over the Late Quaternary

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.608339 ◽

2020 ◽

Vol 8 ◽

Author(s):

Meghana Natesh ◽

K. L. Vinay ◽

Samriddha Ghosh ◽

Rajah Jayapal ◽

Shomita Mukherjee ◽

...

Keyword(s):

Population Size ◽

Effective Population Size ◽

Late Quaternary ◽

Habitat Associations ◽

Interglacial Period ◽

Effective Population ◽

Size Change ◽

Last Glacial ◽

Population Size Estimates ◽

The Last Glacial

Climatic oscillations over the Quaternary have had a lasting impact on species’ distribution, evolutionary history, and genetic composition. Many species show dramatic population size changes coinciding with the last glacial period. However, the extent and direction of change vary across biogeographic regions, species-habitat associations, and species traits. Here we use genomic data to assess population size changes over the late Quaternary using the Pairwise Sequential Markovian Coalescent (PSMC) approach in two Eurasian Owlet species—the Spotted Owlet, Athene brama, and the Jungle Owlet, Glaucidium radiatum. While Spotted Owlets are typically associated with open habitats, Jungle Owlets are found in deciduous forests and scrublands. We find that the effective population size for the Spotted Owlet increased after the Interglacial period till the Last Glacial Maxima and subsequently declined toward the Mid-Holocene. On the other hand, effective population size estimates for the Jungle Owlet increased gradually throughout this period. These observations are in line with climatic niche model-based predictions for range size change for both species from a previous study and suggest that habitat associations at the local scale are important in determining responses to past climatic and vegetational changes. The Spotted Owlet result also aligns well with the expectation of open habitat expansion during the arid Glacial Maxima, whereas for the Jungle Owlet the contrasting expectation does not hold. Therefore, assessing the impacts of glacial history on population trajectories of multiple species with different habitat associations is necessary to understand the impacts of past climate on South Asian taxa.

Download Full-text

The Temporal Dynamics of Background Selection in Nonequilibrium Populations

Genetics ◽

10.1534/genetics.119.302892 ◽

2020 ◽

Vol 214 (4) ◽

pp. 1019-1030 ◽

Cited By ~ 3

Author(s):

Raul Torres ◽

Markus G. Stetter ◽

Ryan D. Hernandez ◽

Jeffrey Ross-Ibarra

Keyword(s):

Natural Selection ◽

Temporal Dynamics ◽

Direct Action ◽

Demographic History ◽

Empirical Studies ◽

Natural Populations ◽

Background Selection ◽

Size Change ◽

Demographic Models ◽

Classical Models

Neutral genetic diversity across the genome is determined by the complex interplay of mutation, demographic history, and natural selection. While the direct action of natural selection is limited to functional loci across the genome, its impact can have effects on nearby neutral loci due to genetic linkage. These effects of selection at linked sites, referred to as genetic hitchhiking and background selection (BGS), are pervasive across natural populations. However, only recently has there been a focus on the joint consequences of demography and selection at linked sites, and some empirical studies have come to apparently contradictory conclusions as to their combined effects. To understand the relationship between demography and selection at linked sites, we conducted an extensive forward simulation study of BGS under a range of demographic models. We found that the relative levels of diversity in BGS and neutral regions vary over time and that the initial dynamics after a population size change are often in the opposite direction of the long-term expected trajectory. Our detailed observations of the temporal dynamics of neutral diversity in the context of selection at linked sites in nonequilibrium populations provide new intuition about why patterns of diversity under BGS vary through time in natural populations and help reconcile previously contradictory observations. Most notably, our results highlight that classical models of BGS are poorly suited for predicting diversity in nonequilibrium populations.

Download Full-text

A RE-EXAMINATION OF LEVELS AND DIFFERENTIAL IN FERTILITY IN SOUTH AFRICA FROM RECENT EVIDENCE

Journal of Biosocial Science ◽

10.1017/s0021932003004139 ◽

2003 ◽

Vol 35 (3) ◽

pp. 413-431 ◽

Cited By ~ 8

Author(s):

ERIC O. UDJO

Keyword(s):

South Africa ◽

Population Size ◽

Total Population ◽

Demographic Models ◽

Final Estimate

The final estimate of South Africa's population as of October 1996 from the first post-apartheid census by Statistics South Africa was lower (40·6 million) than expected (42 million). The expectation of a total population of 42 million was largely based on results of apartheid projections of South Africa's population. The results of the last apartheid census in South Africa in 1991 had been adjusted such that it was consistent with results modelling the population size of South Africa. The discrepancy between the final estimate of the 1996 census and that expected from the modelling described above, and the departure by Statistics South Africa from previous practice of adjusting the census results to be consistent with demographic models, has generated controversies regarding the accuracy of the final results from the 1996 census. This study re-examines levels and differential in fertility in South Africa from recent evidence in order to assess whether or not the fertility inputs in projections of South Africa's population during the apartheid era overestimated fertility.

Download Full-text

Quantifying whether different demographic models produce incongruent results on population dynamics of two long-term studied rodent species

European Journal of Ecology ◽

10.1515/eje-2017-0003 ◽

2017 ◽

Vol 3 (1) ◽

pp. 18-26

Author(s):

Giovanni Amori ◽

Valentina De Silvestro ◽

Paolo Ciucci ◽

Luca Luiselli

Keyword(s):

Population Dynamics ◽

Population Density ◽

Population Size ◽

Myodes Glareolus ◽

Suitable Model ◽

Demographic Model ◽

Apodemus Flavicollis ◽

Demographic Models ◽

Long Term Studies

Abstract1. Population density (ind/ha) of long-term (>15 years) series of CMR populations, using distinct demographic models designed for both open and closed populations, were analysed for two sympatric species of rodents (Myodes glareolus and Apodemus flavicollis) from a mountain area in central Italy, in order to test the relative performance of various employed demographic models. In particular, the hypothesis that enumeration models systematically underestimate the population size of a given population was tested.2. Overall, we compared the performance of 7 distinct demographic models, including both closed and open models, for each study species. Although the two species revealed remarkable intrinsic differences in demography traits (for instance, a lower propensity for being recaptured in Apodemus flavicollis), the Robust Design appeared to be the best fitting model, showing that it is the most suitable model for long-term studies.3. Among the various analysed demographic models, Jolly-Seber returned the lower estimates of population density for both species. Thus, this demographic model could not be suggested for being applied for long-term studies of small mammal populations because it tends to remarkably underestimate the effective population size. Nonetheless, yearly estimates of population density by Jolly-Seber correlated positively with yearly estimates of population density by closed population models, thus showing that interannual trends in population dynamics were uncovered by both types of demographic models, although with different values in terms of true population size.

Download Full-text

PROBABILITY OF FIXATION AND MEAN FIXATION TIME OF AN OVERDOMINANT MUTATION

Genetics ◽

10.1093/genetics/74.2.371 ◽

1973 ◽

Vol 74 (2) ◽

pp. 371-380

Author(s):

Masatoshi Nei ◽

A K Roychoudhury

Keyword(s):

Population Size ◽

Gene Frequency ◽

Finite Population ◽

Retardation Factor ◽

Fixation Time ◽

Selection Intensity ◽

Infinite Population ◽

Probability Of Fixation

ABSTRACT The probability of fixation of an overdominant mutation in a finite population depends on the equilibrium gene frequency in an infinite population (m) and the product (A) of population size and selection intensity. If m < 0.5 (disadvantageous overdominant genes), the probability is generally much lower than that of neutral genes; but if m is close to 0.5 and A is relatively small, it becomes higher. If m > 0.5 (advantageous overdominant genes), the probability is largely determined by the fitness of heterozygotes rather than that of mutant homozygotes. Thus, overdominance enhances the probability of fixation of advantageous mutations. The average number of generations until fixation of an overdominant mutation also depends on m and A. This average time is long when m is close to 0.5 but short when m is close to 0 or 1. This dependence on m and A is similar to that of Robertson's retardation factor.

Download Full-text