scholarly journals Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms

PLoS ONE ◽  
2010 ◽  
Vol 5 (5) ◽  
pp. e10609 ◽  
Author(s):  
C. William Birky ◽  
Joshua Adams ◽  
Marlea Gemmel ◽  
Julia Perry
Keyword(s):  
Dna Sequences ◽  
Population Genetic ◽  
Genetic Theory ◽  
Species Detection ◽  
Detection And Identification

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematodeThoracostoma trachygaster(Nematoda, Leptosomatidae)

2010 ◽  
Vol 39 (3) ◽  
pp. 276-289 ◽  
Author(s):  
Sofie Derycke ◽  
Paul De Ley ◽  
Irma Tandingan De Ley ◽  
Oleksandr Holovachov ◽  
Annelien Rigaux ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Dna Sequences ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Cryptic Diversity

scholarly journals Recombination hotspots as a point process

2005 ◽  
Vol 360 (1460) ◽  
pp. 1597-1603 ◽  
Author(s):  
Maria De Iorio ◽  
Eric de Silva ◽  
Michael P.H Stumpf
Keyword(s):  
Point Process ◽  
Dna Sequences ◽  
Recombination Rate ◽  
Population Genetic ◽  
Process Model ◽  
Chromosomal Dna ◽  
New Approach ◽  
Recombination Hotspots ◽  
Minimum Number ◽  
Fully Bayesian

The variation of the recombination rate along chromosomal DNA is one of the important determinants of the patterns of linkage disequilibrium. A number of inferential methods have been developed which estimate the recombination rate and its variation from population genetic data. The majority of these methods are based on modelling the genealogical process underlying a sample of DNA sequences and thus explicitly include a model of the demographic process. Here we propose a different inferential procedure based on a previously introduced framework where recombination is modelled as a point process along a DNA sequence. The approach infers regions containing putative hotspots based on the inferred minimum number of recombination events; it thus depends only indirectly on the underlying population demography. A Poisson point process model with local rates is then used to infer patterns of recombination rate estimation in a fully Bayesian framework. We illustrate this new approach by applying it to several population genetic datasets, including a region with an experimentally confirmed recombination hotspot.

Quantifying genetic variation at the molecular level

2019 ◽  
pp. 34-66
Author(s):  
Asher D. Cutter
Keyword(s):  
Genetic Variation ◽  
Dna Sequences ◽  
Migration Rate ◽  
Population Genetic ◽  
Quantitative Methods ◽  
Molecular Level ◽  
Effective Population ◽  
Fundamental Properties ◽  
Site Frequency Spectrum ◽  
Population Genetic Variation

Chapter 3, “Quantifying genetic variation at the molecular level,” introduces quantitative methods for measuring variation directly in DNA sequences to help decipher fundamental properties of populations and what they can tell us about evolution. It provides an overview of the evolutionary factors that contribute to genetic variation, like mutational input, effective population size, genetic drift, migration rate, and models of migration. This chapter surveys the principal ways to measure and summarize polymorphisms within a single population and across multiple populations of a species, including heterozygosity, nucleotide polymorphism estimators of θ‎, the site frequency spectrum, and F ST, and by providing illustrative natural examples. Populations are where evolution starts, after mutations arise as the spark of population genetic variation, and Chapter 3 describes how to quantify the variation to connect observations to predictions about how much polymorphism there ought to be under different circumstances.

Population Genetic Theory of the Cost of Inbreeding

1984 ◽  
Vol 123 (5) ◽  
pp. 642-653 ◽  
Author(s):  
Marcus Feldman ◽  
Freddy B. Christiansen
Keyword(s):  
Population Genetic ◽  
Genetic Theory ◽  
The Cost

Species concepts: a contrast of viewpoints

1996 ◽  
Vol 17 (4) ◽  
pp. 295-301
Author(s):  
Günter Gollmann
Keyword(s):  
Population Genetic ◽  
Species Concepts ◽  
Phylogenetic Species ◽  
Genetic Theory ◽  
Pattern And Process ◽  
Genealogical Concordance ◽  
Evolutionary Genetic

AbstractSome fundamental contrasts underlying the disputes about species concepts are outlined: nominalistic versus essentialistic viewpoints, relations of pattern and process, and incongruities of population genetic, ecological, and phylogenetic approaches. The biological, evolutionary and phylogenetic species concepts are briefly characterized. Attention is drawn to the cohesion concept of species and to genealogical concordance principles, which attempt to integrate elements of those concepts with advances in population biological and evolutionary genetic theory.

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