scholarly journals The global population genetics of Dengue viruses revealed through temporal and spatial mapping of viral genetic variation

2016 ◽  
Vol 53 ◽  
pp. 154
Author(s):  
K.D. Kawashima ◽  
H. Akashi
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Spatial Mapping ◽  
Dengue Viruses ◽  
Temporal And Spatial ◽  
Global Population

scholarly journals THE EVOLUTION OF SELECTIVELY SIMILAR ELECTRO-PHORETICALLY DETECTABLE ALLELES IN FINITE NATURAL POPULATIONS

Genetics ◽  
1975 ◽  
Vol 80 (2) ◽  
pp. 375-394
Author(s):  
C F Wehrhahn
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Generating Functions ◽  
Natural Populations ◽  
Net Charge ◽  
Electrophoretic Variants ◽  
Allelic State ◽  
Competing Hypotheses ◽  
State Difference ◽  
General Method

Abstract Most of the models of population genetics are not realistic when applied to data on electrophoretic variants of proteins because the same net charge may result from any of several amino acid combinations. In the absence of realistic models they have, however, been widely used to test competing hypotheses about the origin and maintenance of genetic variation in populations. In this paper I present a general method for determining probability generating functions for electrophoretic state differences. Then I use the method to find allelic state difference distributions for selectively similar electrophoretically detectable alleles in finite natural populations. Predicted patterns of genetic variation, both within and among species, are in reasonable accord with those found in the Drosophila willistoni group by Ayala et al. (1972) and by Ayala and Tracey (1974).

scholarly journals Speciation in the Cladophorales species flock of ancient Lake Baikal

2021 ◽  
Author(s):  
◽  
Sergio Diaz Martinez
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Reproductive Isolation ◽  
Lake Baikal ◽  
Species Delimitation ◽  
Sympatric Speciation ◽  
Species Flock ◽  
Ancient Lake ◽  
Data Set ◽  
Dispersal Abilities

<p>Understanding speciation is one of the great challenges in evolutionary biology as many of the processes involved in speciation, as well as the forces leading to morphological and genetic differentiation, are not fully understood. Three main modes of speciation have been described: allopatric, parapatric and sympatric. Sympatric speciation is the most enigmatic mode because in the absence of physical barriers, disruptive selection, assortative mating and hybridization play central roles in reproductive isolation. Although it is accepted that sympatric speciation is possible, only a few examples of this process exist to date. Another common method of speciation in plants and algae is via polyploidization. Recently, a promising system to study speciation in sympatry was discovered: the endemic Cladophorales species flock in ancient Lake Baikal, Russia. The flock consists of sixteen taxa grouped in four genera: Chaetocladiella, Chaetomorpha, Cladophora and Gemmiphora. In spite of their morphological diversity, recent molecular analyses have shown that this is a monophyletic group with low genetic variation and nested within the morphologically simple genus Rhizoclonium. Due to their high number of species, endemism and sympatric distribution, many interesting questions have arisen such as what processes are involved in speciation, and whether this group might be a novel example of sympatric speciation. In this study, we analysed the population genetics of the endemic Baikalian Cladophorales to infer the processes shaping the evolution of the group. First, a set of microsatellites was designed using high-throughput sequencing data. Second, species delimitation methods based on genetic clustering were performed. Third, the population genetics of three widely distributed species was analysed looking for evidence of panmixia, a common criteria to support sympatric speciation. A total of 11 microsatellites that mostly cross-amplify between most species were obtained. The genotyping revealed that most loci had more than two alleles per individual indicating polyploidy. As such, the analyses required a different approach which consisted in coding the genotypes as ‘allelic phenotypes’, allowing the use of individuals of different ploidy levels in the same data set. The species delimitation of 15 operative morphotaxa and 727 individuals supported reproductive isolation of five morphotaxa and two hypotheses of conspecificity. However, some morphotaxa showed unclear assignments revealing the need of further research to clarify their reproductive limits. Finally, the population genetics of Chaetomorpha moniliformis, Cladophora compacta and Cl. kursanovii revealed patterns of genetic variation and structure that suggest different reproductive strategies and dispersal abilities. This demonstrates that contrasting biological characteristics may arise in closely related lineages: Chaetomorpha moniliformis with dominant asexual reproduction and long dispersal abilities; Cladophora compacta with high genetic diversity, no population structure and likely to reproduce sexually; Cl. kursanovii with a structure congruent with geographic distribution and more restricted dispersal. The results suggest that polyploidy, rather than speciation with gene flow, is the force driving the reproductive isolation and evolution of this flock. Although many questions remain to be studied, this research provides the first insights into the diversification of this Cladophorales species flock and contributes to the understanding of speciation in freshwater algae.</p>

scholarly journals Artificial selection and maintenance of genetic variance in the global dairy cow population

2005 ◽  
Vol 360 (1459) ◽  
pp. 1479-1488 ◽  
Author(s):  
S Brotherstone ◽  
M Goddard
Keyword(s):  
Genetic Variation ◽  
Genetic Improvement ◽  
Breeding Value ◽  
Payment Systems ◽  
Frozen Semen ◽  
Best Linear Unbiased ◽  
The Uk ◽  
Selection Algorithms ◽  
Global Population

Genetic improvement of dairy cows, which has increased the milk yield of cows in the UK by 1200 kg per lactation in 12 years, is an excellent example of the application of quantitative genetics to agriculture. The most important traits of dairy cattle are expressed only in females, but the main opportunity for selection is in males. Despite this, genetic improvement was achieved by the invention of a new statistical methodology, called ‘best linear unbiased prediction’ to estimate the breeding value of bulls. Intense selection of the best bulls, combined with the worldwide use of these bulls through artificial insemination and frozen semen, has created a global population and caused concern that the genetic variation available in the future will be reduced. Maintenance of genetic variation and long-term genetic gains would be aided by rational payment systems, use of crossbreeding where profitable, inclusion of all economically important traits in the breeding objective, recognition of genotype by environment interactions and the use of selection algorithms that balance estimated breeding value against the average relationship among the selected animals. Fortunately, all of these things are happening to some degree.

scholarly journals The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1273
Author(s):  
Katherine Parker ◽  
A. Mesut Erzurumluoglu ◽  
Santiago Rodriguez
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Y Chromosome ◽  
Complex Traits ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Complex Locus ◽  
Complex Human Traits ◽  
Human Complex ◽  
Human Y Chromosome

The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.

Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Genome ◽  
2014 ◽  
Vol 57 (4) ◽  
pp. 239-244 ◽  
Author(s):  
Xifeng Ren ◽  
Yonggang Wang ◽  
Songxian Yan ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Population Genetics ◽  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Hordeum Vulgare ◽  
Nucleotide Diversity ◽  
Wild Barley ◽  
Haplotype Diversity ◽  
Lateral Spikelet ◽  
Cultivated Barley ◽  
Barley Population

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

Random partitions in population genetics

1978 ◽  
Vol 361 (1704) ◽  
pp. 1-20 ◽  
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Charge State ◽  
Characteristic Property ◽  
Large Population ◽  
Recurrent Mutation ◽  
Random Partitions ◽  
Ewens Sampling Formula ◽  
Sampling Formula ◽  
State Models

This paper is concerned with models for the genetic variation of a sample of gametes from a large population. The need for consistency between different sample sizes limits the mathematical possibilities to what are here called ‘partition structures Distinctive among them is the structure described by the Ewens sampling formula, which is shown to enjoy a characteristic property of non-interference between the different alleles. This characterization explains the robustness of the Ewens formula when neither selection nor recurrent mutation is significant, although different structures arise from selective and ‘charge-state’ models

scholarly journals Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Malinee Anantaphruti ◽  
Urusa Thaenkham ◽  
Teera Kusolsuk ◽  
Wanna Maipanich ◽  
Surapol Saguankiat ◽  
...  
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Endangered Species ◽  
Selective Sweep ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
World Population ◽  
Taenia Saginata ◽  
Northeast Thailand ◽  
Haplotype A

Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. saginataworld population, suggesting population expansion. Significant Fu’sFsvalues in Thai, as well as world population, also indicate that population is expanding and may be hitchhiking as part of selective sweep. Haplotype B and its dispersion were only found in populations from Thailand. Haplotype B may evolve and ultimately become an ancestor of future populations in Thailand. Haplotype A seems to be dispersion haplotype, not just in Thailand, but worldwide. High geneticT. saginataintraspecies divergence was found, in contrast to its sister species,T. asiatica; among 30 samples from seven countries, its haplotype diversity was 0.067, while only 2 haplotypes were revealed. This extremely low intraspecific variation suggests thatT. asiaticacould be an endangered species.

scholarly journals Causes of natural variation in fitness: Evidence from studies of Drosophila populations

2015 ◽  
Vol 112 (6) ◽  
pp. 1662-1669 ◽  
Author(s):  
Brian Charlesworth
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Balancing Selection ◽  
Large Contribution ◽  
Deleterious Mutations ◽  
Weak Selection ◽  
Fitness Components ◽  
Genetic Studies ◽  
Standing Variation ◽  
Available Information

DNA sequencing has revealed high levels of variability within most species. Statistical methods based on population genetics theory have been applied to the resulting data and suggest that most mutations affecting functionally important sequences are deleterious but subject to very weak selection. Quantitative genetic studies have provided information on the extent of genetic variation within populations in traits related to fitness and the rate at which variability in these traits arises by mutation. This paper attempts to combine the available information from applications of the two approaches to populations of the fruitfly Drosophila in order to estimate some important parameters of genetic variation, using a simple population genetics model of mutational effects on fitness components. Analyses based on this model suggest the existence of a class of mutations with much larger fitness effects than those inferred from sequence variability and that contribute most of the standing variation in fitness within a population caused by the input of mildly deleterious mutations. However, deleterious mutations explain only part of this standing variation, and other processes such as balancing selection appear to make a large contribution to genetic variation in fitness components in Drosophila.

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