scholarly journals In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Vaishali Katju
Keyword(s):  
Gene Duplication ◽  
Population Size ◽  
Population Genetic ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Dna And Rna ◽  
Duplication Events ◽  
History Of ◽  
Theoretical Population ◽  
Novel Exon

The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno’s formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno’s model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (Ne) of a species may influence the probability of emergence of genes with radically altered functions.

scholarly journals Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 779
Author(s):  
Santos ◽  
Fernandes ◽  
Henley ◽  
Dawson ◽  
Mumby
Keyword(s):  
Population Size ◽  
National Park ◽  
Genetic Bottleneck ◽  
Kruger National Park ◽  
Time Lags ◽  
Limited Information ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Starting Point ◽  
Demographic Bottleneck

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500–700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

scholarly journals Coalescence theory for a general class of structured populations with fast migration

2011 ◽  
Vol 43 (04) ◽  
pp. 1027-1047 ◽  
Author(s):  
O. Hössjer
Keyword(s):  
Population Size ◽  
General Class ◽  
Population Genetic ◽  
Total Population ◽  
Structured Populations ◽  
Effective Population ◽  
Constant Change ◽  
Skorokhod Topology ◽  
Age Structured ◽  
Dependency Structures

In this paper we study a general class of population genetic models where the total population is divided into a number of subpopulations or types. Migration between subpopulations is fast. Extending the results of Nordborg and Krone (2002) and Sagitov and Jagers (2005), we prove, as the total population sizeNtends to ∞, weak convergence of the joint ancestry of a given sample of haploid individuals in the Skorokhod topology towards Kingman's coalescent with a constant change of time scalec. Our framework includes age-structured models, geographically structured models, and combinations thereof. We also allow each individual to have offspring in several subpopulations, with general dependency structures between the number of offspring of various types. As a byproduct, explicit expressions for the coalescent effective population sizeN/care obtained.

scholarly journals Recombination Gives a New Insight in the Effective Population Size and the History of the Old World Human Populations

2011 ◽  
Vol 29 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Marta Melé ◽  
Asif Javed ◽  
Marc Pybus ◽  
Pierre Zalloua ◽  
Marc Haber ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Populations ◽  
Effective Population ◽  
Old World ◽  
History Of

scholarly journals Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

2019 ◽  
Vol 110 (5) ◽  
pp. 587-600
Author(s):  
A Millie Burrell ◽  
Jeffrey H R Goddard ◽  
Paul J Greer ◽  
Ryan J Williams ◽  
Alan E Pepper
Keyword(s):  
Gene Flow ◽  
Genetic Connectivity ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Isolated Populations ◽  
Long Distance ◽  
Population Sizes ◽  
History Of ◽  
Small Set ◽  
Nuclear Microsatellite

Abstract Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne &lt; 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., &gt;1 km), possibly via zoochory.

scholarly journals Time for spreading of compensatory mutations under gene duplication.

Genetics ◽  
1989 ◽  
Vol 123 (3) ◽  
pp. 579-584
Author(s):  
T Ohta
Keyword(s):  
Gene Duplication ◽  
Diffusion Equation ◽  
Population Size ◽  
Computer Simulations ◽  
Deleterious Mutation ◽  
Selective Constraint ◽  
Effective Population ◽  
Gene Redundancy ◽  
Tight Linkage ◽  
Compensatory Mutations

Abstract Evolution by compensatory mutations is accelerated by gene duplication because selective constraint is relaxed by gene redundancy. A mutation is called compensatory if it corrects the effect of an earlier deleterious mutation. Without duplication, Kimura has shown that the time for spreading of compensatory mutations is much reduced by tight linkage between the two chromosomal sites of mutations. In this report, the time for spreading with gene duplication was studied by using the diffusion equation method of Kimura, together with computer simulations. It was shown that, when 2Nv- is much less than unity, the time for spreading is greatly shortened by gene duplication as compared with the case of complete linkage between the two sites of mutations, where 2N is the effective population size (haploid) and v- is the rate of compensatory mutations. However, if 2Nv- greater than 1, gene duplication is not effective for accelerating the evolution by such mutations.

scholarly journals Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1236
Author(s):  
Elisabeth Hempel ◽  
Michael V. Westbury ◽  
José H. Grau ◽  
Alexandra Trinks ◽  
Johanna L. A. Paijmans ◽  
...  
Keyword(s):  
Population Size ◽  
Population History ◽  
Phylogeographic Structure ◽  
Recent Common Ancestor ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Mammal Species ◽  
Human Disturbances ◽  
Most Recent Common Ancestor ◽  
History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

scholarly journals Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine (Pinus strobus): Conservation Value and Climate Adaptation Potential

2021 ◽  
Vol 12 ◽  
Author(s):  
Om P. Rajora ◽  
John W. R. Zinck
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Conservation Value ◽  
Adaptive Potential ◽  
Effective Population ◽  
White Pine ◽  
Old Growth ◽  
Second Growth

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

scholarly journals Introgression makes waves in inferred histories of effective population size

2017 ◽  
Author(s):  
John Hawks
Keyword(s):  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
History Of ◽  
Or Gene ◽  
Time Of Origin ◽  
Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

scholarly journals Approximating the coalescent under facultative sex

2019 ◽  
Author(s):  
Matthew Hartfield
Keyword(s):  
Population Size ◽  
Evolutionary History ◽  
Sampling Strategies ◽  
Effective Population ◽  
Sexual Species ◽  
History Of ◽  
Mitotic Gene Conversion ◽  
Evolutionary Consequences ◽  
Insight Into ◽  
Coalescent Time

AbstractGenome studies of facultative sexual species, which can either reproduce sexually or asexually, are providing insight into the evolutionary consequences of mixed reproductive modes. It is currently unclear to what extent the evolutionary history of facultative sexuals’ genomes can be approximated by the standard coalescent, and if a coalescent effective population size Ne exists. Here, I determine if and when these approximations can be made. When sex is frequent (occurring at a frequency much greater than 1/N per reproduction per generation, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent, with a coalescent Ne ≈ N. When sex is very rare (at frequency much lower than 1/N), approximations for the pairwise coalescent time can be obtained, which is strongly influenced by the frequencies of sex and mitotic gene conversion, rather than N. However, these terms do not translate into a coalescent Ne. These results are used to discuss the best sampling strategies for investigating the evolutionary history of facultative sexual species.

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