scholarly journals Updates in the Language ofHistoplasmaBiodiversity

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Pierre Gladieux
Keyword(s):  
Evolutionary History ◽  
Species Recognition ◽  
Fungal Species ◽  
Species Status ◽  
Genome Resequencing ◽  
Intraspecific Divergence ◽  
Testing Framework ◽  
Population Genomic ◽  
History Of ◽  
Whole Genome Resequencing

ABSTRACTIn a recent article, Sepúlveda et al. (mBio 8:e01339-17, 2017, https://doi.org/10.1128/mBio.01339-17) investigated the genetic structure and evolutionary history of the human pathogenHistoplasma. Using whole-genome resequencing data, Sepúlveda et al. found that theHistoplasmagenus is composed of at least four strongly differentiated lineages. Their tour de force is to use a smart combination of population genomic approaches to show that the advanced stage of intraspecific divergence observed withinHistoplasmadoes not simply reflect population structure, but instead results from previously unidentified speciation events. The four independently evolvingHistoplasmalineages are elevated to the species status and assigned names. The newly described species exhibit medically important differences in phenotype, and these findings, therefore, have important epidemiological implications. This work provides a blueprint for phylogenomic species recognition in fungi, opening the way for a new age of enlightenment in which fungal species are diagnosed using highly discriminatory tools within a hypothesis-testing framework.

scholarly journals Linked-read sequencing enables haplotype-resolved resequencing at population scale

2020 ◽  
Author(s):  
Dave Lutgen ◽  
Raphael Ritter ◽  
Remi-André Olsen ◽  
Holger Schielzeth ◽  
Joel Gruselius ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
Genome Resequencing ◽  
High Coverage ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of ◽  
Population Scale ◽  
Haplotype Information

AbstractThe feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and the inference of selective sweeps – are still limited by the lack of high-quality haplotype information. In this respect, the newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of the phased sequence located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90), respectively. Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Finally, phasing contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing data at population scale.

scholarly journals Evidence of post-domestication hybridization and adaptive introgression in Western European grapevine varieties

2021 ◽  
Author(s):  
S. Freitas ◽  
M.A. Gazda ◽  
M. Rebelo ◽  
A.J. Muñoz-Pajares ◽  
C. Vila-Viçosa ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Western Europe ◽  
Study Group ◽  
Wild Populations ◽  
Genome Resequencing ◽  
Adaptive Introgression ◽  
The World ◽  
History Of ◽  
Whole Genome Resequencing ◽  
Historical Periods

ABSTRACTGrapevine (Vitis vinifera L.) is one of the most significant crops in the world. Today’s richness in grapevine diversity results from a complex domestication history over multiple historical periods. Here, we employed whole genome resequencing to elucidate different aspects of the recent evolutionary history of this crop. Our results support a model in which a central domestication event in grapevine was followed by post-domestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties, which show large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by geneflow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

scholarly journals Inferring the evolutionary history of Populus trichocarpa from whole genome resequencing data

2011 ◽  
Vol 5 (S7) ◽  
Author(s):  
Stephen DiFazio ◽  
Gancho Slavov ◽  
Eli Rodgers-Melnick ◽  
Joel Martin ◽  
Wendy Schackwitz ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Populus Trichocarpa ◽  
Whole Genome ◽  
Genome Resequencing ◽  
History Of ◽  
Whole Genome Resequencing

scholarly journals No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 58 ◽  
Author(s):  
Martin Irestedt ◽  
Per G. P. Ericson ◽  
Ulf S. Johansson ◽  
Paul Oliver ◽  
Leo Joseph ◽  
...  
Keyword(s):  
19Th Century ◽  
Evolutionary History ◽  
Genetic Erosion ◽  
Glacial Cycle ◽  
Genome Resequencing ◽  
Extrinsic Factors ◽  
Dramatic Decline ◽  
Whole Genome Resequencing ◽  
The 19Th Century ◽  
The Last Glacial

The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.

scholarly journals Author Correction: Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Jason D. Hoeksema ◽  
James D. Bever ◽  
Sounak Chakraborty ◽  
V. Bala Chaudhary ◽  
Monique Gardes ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Fungal Species ◽  
Fixed Effect ◽  
Correct Description ◽  
Soil Inoculum ◽  
Plant Hosts ◽  
History Of ◽  
Fungal Genus

In the original published version of the article, the description of the fixed-effect predictor Inoculum Complexity presented in the Methods was incorrect. The incorrect description given was: “single fungal genus, multiple fungal genera, or whole soil inoculum”. The correct description is: “single fungal species, multiple fungal species, or whole soil inoculum”. The error does not affect any of the results presented in the paper. The correction has been made to the HTML and PDF versions of the paper.

scholarly journals A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

2009 ◽  
Vol 75 (16) ◽  
pp. 5410-5416 ◽  
Author(s):  
Gabriele Margos ◽  
Stephanie A. Vollmer ◽  
Muriel Cornet ◽  
Martine Garnier ◽  
Volker Fingerle ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Lyme Borreliosis ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Housekeeping Genes ◽  
Multilocus Sequence Analysis ◽  
Species Status ◽  
Borrelia Garinii ◽  
Analysis Scheme ◽  
History Of

ABSTRACT Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.

scholarly journals Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize

2020 ◽  
Author(s):  
Jonás A. Aguirre-Liguori ◽  
Javier A. Luna-Sánchez ◽  
Jaime Gasca-Pineda ◽  
Luis E. Eguiarte
Keyword(s):  
Evolutionary History ◽  
Isolation By Distance ◽  
Molecular Ecology ◽  
Population Genomic ◽  
History Of ◽  
Outlier Tests ◽  
Landscape Genetic ◽  
Genomic Regions ◽  
Computational Resources ◽  
Number Of Individuals

ABSTRACTMassive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens

2020 ◽  
pp. PHYTO-07-20-031
Author(s):  
David A. Rasmussen ◽  
Niklaus J. Grünwald
Keyword(s):  
Evolutionary History ◽  
Plant Pathogens ◽  
Geographic Information ◽  
Geographic Context ◽  
Population Genomic ◽  
History Of

Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.

scholarly journals Minimal-assumption inference from population-genomic data

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Daniel B Weissman ◽  
Oskar Hallatschek
Keyword(s):  
Evolutionary History ◽  
Simulated Data ◽  
Large Samples ◽  
Minimal Assumption ◽  
Population Genomic ◽  
Human Genomes ◽  
History Of ◽  
Or Gene ◽  
Linked Selection ◽  
Genomic Length

Samples 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. 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 coalescence or recombination, allowing it to analyze arbitrarily large samples without phasing while making no assumptions about ancestral structure, linked selection, or gene conversion. Using simulated data, we show that the performance of MAGIC is comparable to that of PSMC’ even on single diploid samples generated with standard coalescent and recombination models. Applying MAGIC to a sample of human genomes reveals evidence of non-demographic factors driving coalescence.

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