Evolutionary Genomics of High Fecundity

2020 ◽  
Vol 54 (1) ◽  
pp. 213-236
Author(s):  
Bjarki Eldon
Keyword(s):  
Population Genetics ◽  
Population Genetic ◽  
Reference Model ◽  
Evolutionary Genomics ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
High Fecundity ◽  
Large Numbers ◽  
Fisher Model ◽  
Evolutionary Studies

Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright–Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright–Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright–Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright–Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.

scholarly journals PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives

2021 ◽  
Author(s):  
José Gonçalves-Dias ◽  
Markus G Stetter
Keyword(s):  
Interdisciplinary Research ◽  
Population Genetic ◽  
Genetic Research ◽  
Wild Relatives ◽  
Genome Browser ◽  
Reference Sequence ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Grain Amaranth ◽  
Amaranth Species

Abstract The combination of genomic, physiological, and population genetic research has accelerated the understanding and improvement of numerous crops. For non-model crops the lack of interdisciplinary research hinders their improvement. Grain amaranth is an ancient nutritious pseudocereal that has been domesticated three times in different regions of the Americas. We present and employ PopAmaranth, a population genetic genome browser, which provides an accessible representation of the genetic variation of the three grain amaranth species (A. hypochondriacus, A. cruentus, and A. caudatus) and two wild relatives (A. hybridus and A. quitensis) along the A. hypochondriacus reference sequence. We performed population-scale diversity and selection analysis from whole-genome sequencing data of 88 curated genetically and taxonomically unambiguously classified accessions. We employ the platform to show that genetic diversity in the water stress-related MIF1 gene declined during amaranth domestication and provide evidence for convergent saponin reduction between amaranth and quinoa. PopAmaranth is available through amaranthGDB at amaranthgdb.org/popamaranth.html.

scholarly journals rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)

2020 ◽  
Vol 10 (9) ◽  
pp. 3041-3046
Author(s):  
Silas Tittes
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Population Genetic ◽  
R Package ◽  
Ease Of Use ◽  
Software Implementation ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Comprehensive Overview

Abstract The availability of whole genome sequencing data from multiple related populations creates opportunities to test sophisticated population genetic models of convergent adaptation. Recent work by Lee and Coop (2017) developed models to infer modes of convergent adaption at local genomic scales, providing a rich framework for assessing how selection has acted across multiple populations at the tested locus. Here I present, rdmc, an R package that builds on the existing software implementation of Lee and Coop (2017) that prioritizes ease of use, portability, and scalability. I demonstrate installation and comprehensive overview of the package’s current utilities.

scholarly journals STR loci D19S216, D20S502 and D20S842 analysis in the Serbian population using dentin DNA

2011 ◽  
Vol 63 (1) ◽  
pp. 55-58
Author(s):  
Dragana Puzovic ◽  
D. Dunjic ◽  
Branka Popovic ◽  
O. Stojkovic ◽  
Ivana Novakovic ◽  
...  
Keyword(s):  
Population Genetics ◽  
Mitochondrial Dna ◽  
Population Genetic ◽  
Genetic Studies ◽  
Str Loci ◽  
Large Numbers ◽  
Forensic Case ◽  
Case Work

Dentin provides a protective enclosure for genomic and mitochondrial DNA. In the present study, DNA was obtained from pulverized or ground teeth. The quality of the DNA extracted from the teeth of 70 unrelated individuals was tested in the context of assessing the allelic and genotypic frequencies of autosomal loci D19S216, D20S502 and D20S842, and calculating a number of parameters of population genetics and forensic interest. This study illustrates that teeth can be a convenient tissue to extract DNA from large numbers of individuals for population genetic studies as well as for forensic case work.

Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution

Parasitology ◽  
2006 ◽  
Vol 134 (2) ◽  
pp. 153-167 ◽  
Author(s):  
R. SHAO ◽  
S. C. BARKER
Keyword(s):  
Population Genetics ◽  
Population Genetic ◽  
Current Knowledge ◽  
Mitochondrial Genes ◽  
Nucleotide Sequences ◽  
Future Research ◽  
Mitochondrial Genomes ◽  
Genomic Features ◽  
Coding Regions ◽  
Evolutionary Studies

Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes, cox1, cob, rrnS and rrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.

scholarly journals PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Chao Zhang ◽  
Yang Gao ◽  
Zhilin Ning ◽  
Yan Lu ◽  
Xiaoxi Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Genetic Variants ◽  
Population Genetic ◽  
Unique Feature ◽  
Indigenous Populations ◽  
Diverse Populations ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Single Nucleotide Variations

Abstract Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution, we developed a database, PGG.SNV (https://www.pggsnv.org), which gives much higher weight to previously under-investigated indigenous populations in Asia. PGG.SNV archives 265 million SNVs across 220,147 present-day genomes and 1018 ancient genomes, including 1009 newly sequenced genomes, representing 977 global populations. Moreover, estimation of population genetic diversity and evolutionary parameters is available in PGG.SNV, a unique feature compared with other databases.

scholarly journals rdmc: an open source R package implementing convergent adaptation models of Lee and Coop (2017)

2020 ◽  
Author(s):  
Silas Tittes
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Population Genetic ◽  
R Package ◽  
Ease Of Use ◽  
Software Implementation ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Comprehensive Overview

ABSTRACTThe availability of whole genome sequencing data from multiple related populations creates opportunities to test sophisticated population genetic models of convergent adaptation. Recent work by Lee and Coop (2017) developed models to infer modes of convergent adaption at local genomic scales, providing a rich framework for assessing how selection has acted across multiple populations at the tested locus. Here I present, rdmc, an R package that builds on the existing software implementation of Lee and Coop (2017) that prioritizes ease of use, portability, and scalability. I demonstrate installation and comprehensive overview of the package’s current utilities.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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