scholarly journals Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 266 ◽  
Author(s):  
Brian Park ◽  
John M. Burke
Keyword(s):  
Genetic Variation ◽  
Helianthus Annuus ◽  
Great Plains ◽  
Evolutionary History ◽  
Nucleotide Diversity ◽  
Secondary Development ◽  
Effective Population ◽  
Comprehensive Overview ◽  
Helianthus Annuus L ◽  
History Of

Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species

2018 ◽  
Author(s):  
Robert D. Denton ◽  
Ariadna E. Morales ◽  
H. Lisle Gibbs
Keyword(s):  
Genetic Variation ◽  
Evolutionary History ◽  
Parental Species ◽  
Extended Period ◽  
Reproductive Mode ◽  
Mapping Method ◽  
Genetic Introgression ◽  
Sexual Species ◽  
History Of ◽  
Genomic Material

AbstractQuantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations—variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ∼3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.

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.

scholarly journals Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava

2020 ◽  
Vol 14 (6) ◽  
pp. 1333-1344
Author(s):  
Romain Savary ◽  
Cindy Dupuis ◽  
Frédéric G. Masclaux ◽  
Ivan D. Mateus ◽  
Edward C. Rojas ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Food Security ◽  
Evolutionary History ◽  
Mycorrhizal Fungus ◽  
History Of

Lack of genetic variability in French identified races of Plasmopara halstedii, the cause of downy mildew in sunflower Helianthus annuus

1997 ◽  
Vol 43 (3) ◽  
pp. 260-263 ◽  
Author(s):  
Patricia Roeckel-Drevet ◽  
Véronique Coelho ◽  
Paul Nicolas ◽  
Jeanne Tourvieille ◽  
Denis Tourvieille de Labrouhe
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Helianthus Annuus ◽  
Downy Mildew ◽  
Random Amplified Polymorphic Dna ◽  
Initial Screening ◽  
Plasmopara Halstedii ◽  
Helianthus Annuus L ◽  
New Races

Downy mildew of sunflower (Helianthus annuus L.) incitated by Plasmopara halstedii is a potentially devastating disease. We report here the finding of two new races of P. halstedii and also two Apron35S fungicide-resistant isolates of race A. Using the random amplified polymorphic DNA (RAPD) technique as an initial screening for genetic variation within P. halstedii French races, genetic variation was not found between isolates within races 1, A, or B, and very few polymorphisms were distinguished between all French races known today.Key words: Plasmopara halstedii, race, genetic variability, RAPD.

scholarly journals Evidence for Genetic Hitchhiking Effect Associated With Insecticide Resistance in Aedes aegypti

Genetics ◽  
1998 ◽  
Vol 148 (2) ◽  
pp. 793-800
Author(s):  
Guiyun Yan ◽  
Dave D Chadee ◽  
David W Severson
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Aedes Aegypti ◽  
Evolutionary History ◽  
Large Fraction ◽  
Target Site ◽  
Chromosome 1 ◽  
Disease Epidemiology ◽  
Length Polymorphisms ◽  
History Of

Abstract Information on genetic variation within and between populations is critical for understanding the evolutionary history of mosquito populations and disease epidemiology. Previous studies with Drosophila suggest that genetic variation of selectively neutral loci in a large fraction of genome may be constrained by fixation of advantageous mutations associated with hitchhiking effect. This study examined restriction fragment length polymorphisms of four natural Aedes aegypti mosquito populations from Trinidad and Tobago, at 16 loci. These populations have been subjected to organophosphate (OP) insecticide treatments for more than two decades, while dichlor-diphenyltrichlor (DDT) was the insecticide of choice prior to this period. We predicted that genes closely linked to the OP target loci would exhibit reduced genetic variation as a result of the hitchhiking effect associated with intensive OP insecticide selection. We also predicted that genetic variability of the genes conferring resistance to DDT and loci near the target site would be similar to other unlinked loci. As predicted, reduced genetic variation was found for loci in the general chromosomal region of a putative OP target site, and these loci generally exhibited larger FST values than other random loci. In contrast, the gene conferring resistance to DDT and its linked loci show polymorphisms and genetic differentiation similar to other random loci. The reduced genetic variability and apparent gene deletion in some regions of chromosome 1 likely reflect the hitchhiking effect associated with OP insecticide selection.

scholarly journals Minimal-assumption inference from population-genomic data

2016 ◽  
Author(s):  
Daniel B. Weissman ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary History ◽  
Simulated Data ◽  
Effective Population ◽  
Minimal Assumption ◽  
Genome Data ◽  
Human Genomes ◽  
Single Genome ◽  
Linkage Information ◽  
Time Histories ◽  
History Of

AbstractSamples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting the sample sizes and populations that they can analyze. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of recombination, demography or selection. Using simulated data, we show that MAGIC’s performance is comparable to PSMC’ on single diploid samples generated with standard coalescent and recombination models. More importantly, MAGIC can also analyze arbitrarily large samples and is robust to changes in the coalescent and recombination processes. Using MAGIC, we show that the inferred coalescence time histories of samples of multiple human genomes exhibit inconsistencies with a description in terms of an effective population size based on single-genome data.

scholarly journals Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

2021 ◽  
Vol 288 (1943) ◽  
pp. 20202934
Author(s):  
Jiaming Hu ◽  
Michael V. Westbury ◽  
Junxia Yuan ◽  
Zhen Zhang ◽  
Shungang Chen ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Wide Range ◽  
Two Samples ◽  
Spotted Hyenas ◽  
History Of ◽  
Close Relatives

Cave hyenas (genus Crocuta ) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta . Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta . Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

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