scholarly journals Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

2017 ◽  
Vol 26 (4) ◽  
pp. 1131-1147 ◽  
Author(s):  
Brittany S. Barker ◽  
Krikor Andonian ◽  
Sarah M. Swope ◽  
Douglas G. Luster ◽  
Katrina M. Dlugosch
Keyword(s):  
Range Expansion ◽  
Centaurea Solstitialis ◽  
Yellow Starthistle ◽  
Trait Evolution ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of

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 Factors Affecting Infection of Yellow Starthistle (Centaurea solstitialis) by Synchytrium solstitiale, Causal Agent of False Rust Disease

Plant Disease ◽  
2006 ◽  
Vol 90 (4) ◽  
pp. 425-428 ◽  
Author(s):  
T. L. Widmer ◽  
F. Guermache
Keyword(s):  
United States ◽  
Classical Biological Control ◽  
The United States ◽  
Carthamus Tinctorius ◽  
Centaurea Solstitialis ◽  
Yellow Starthistle ◽  
Rust Disease ◽  
Invasive Weed ◽  
Factors Affecting ◽  
Centaurea Calcitrapa

Yellow starthistle (Centaurea solstitialis) is an annual invasive weed in the United States with Mediterranean origins. The expense of chemical control and the vast area of invasion make this weed an appropriate target for classical biological control. Observations of a field site in southern France revealed small orange galls on the leaves of yellow starthistle seedlings caused by the fungus Synchytrium solstitiale. Inoculation of yellow starthistle seedlings with a suspension of zoospores released from infected tissue resulted in infection. Ten days after inoculation, typical orange galls appeared on the exposed tissue. Preliminary host range testing showed up to 100% infection of C. solstitialis seedlings from both France and the United States and infection of Carthamus tinctorius, Centaurea americana, C. diffusa, C. rothrockii, C. squarrosa, and Helianthus annuus seedlings. No symptoms were observed on seedlings of Centaurea calcitrapa, C. maculosa, C. sulfurea, Cirsium californica, C. occidentale, Cynera cardunculus, and Taraxacum officinale. Zoospores were released in a pH range between 4.45 and 8.25 and optimally at temperatures between 5 and 15°C. Infection of yellow starthistle seedlings occurred after a minimum 1-h exposure to a zoospore suspension at 20°C.

scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

Range expansion of Ixodes scapularis in the USA.

2021 ◽  
pp. 176-182
Author(s):  
Durland Fish
Keyword(s):  
Range Expansion ◽  
Ixodes Scapularis ◽  
The Usa ◽  
History Of

Abstract This chapter covers the history of Ixodes scapularis, its mode and major pathways of range expansion, and the establishment of I. scapularis-borne pathogens in the USA.

scholarly journals Phylogeography of the California Thrasher (Toxostoma Redivivum) Based on Nested-Clade Analysis of Mitochondrial-DNA Variation

The Auk ◽  
2003 ◽  
Vol 120 (2) ◽  
pp. 346-361
Author(s):  
Erik A. Sgariglia ◽  
Kevin J. Burns
Keyword(s):  
Mitochondrial Dna ◽  
Range Expansion ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Nested Clade Analysis ◽  
Dna Variation ◽  
History Of ◽  
Past Fragmentation ◽  
Intraspecific Relationships ◽  
Geologic Data

Abstract Distribution of genealogical lineages within a species is likely the result of a complicated series of ecological and historical events. Nested-clade analysis is specifically designed as an objective phylogeographic approach for inferring evolutionary processes on a spatial and temporal scale for small subclades within a larger set of intraspecific relationships. Here, we use nested-clade analysis as well as other phylogeographic methods to investigate the evolutionary history of California Thrasher (Toxostoma redivivum) populations. Inferences resulting from nested clade analysis suggest a history that includes past fragmentation, range expansion, and isolation-by-distance. Along with root information, those inferences enable the construction of a biogeographic scenario for this species involving general southern ancestry, an early north–south division, northward range expansion, and a southward back-expansion into an already populated southern region. Isolation-by-distance is also identified, particularly in southern California, indicating that gene flow between localities does occur but is restricted. Many conclusions drawn from this study are concordant with geologic data as well as phylogeographic scenarios drawn for other codistributed California taxa.

scholarly journals An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
João PL Castro ◽  
Michelle N Yancoskie ◽  
Marta Marchini ◽  
Stefanie Belohlavy ◽  
Layla Hiramatsu ◽  
...  
Keyword(s):  
Bone Growth ◽  
Rapid Evolution ◽  
Genomic Analysis ◽  
Selection Response ◽  
Major Effect ◽  
Selection Experiment ◽  
Genomic Analyses ◽  
Selection Experiments ◽  
Polygenic Adaptation ◽  
History Of

Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.

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.

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