The North American Plums (Prunus Spp.): A Review of the Taxonomic and Phylogenetic Relationships

Prunus ◽  
2020 ◽  
Author(s):  
Dario J. Chavez ◽  
José X. Chaparro
Keyword(s):  
Genetic Diversity ◽  
North American ◽  
Fruit Size ◽  
Chilling Requirement ◽  
Prunus Species ◽  
The North ◽  
Phylogenetic Studies ◽  
Center Of Diversity ◽  
Heat Requirement ◽  
Prunus Spp

North America is a center of diversity for Prunus species. Tree architecture, chilling requirement, heat requirement, fruit development period, fruit size, fruit texture, disease resistance, and adaptive changes to multiple environmental conditions are a few examples of the traits of which tremendous genetic variability is available in the native plum species. Wild native Prunus species constitute an important potential source of genetic diversity for stone fruit breeding and selection. A review of the North American plum taxonomic treatment and phylogenetic studies is described. Various studies have been done with three major groups being identified: Americana series, Chickasaw series, and Beach series.

scholarly journals A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 720-732 ◽  
Author(s):  
Kasey K. Pham ◽  
Andrew L. Hipp ◽  
Paul S. Manos ◽  
Richard C. Cronn
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Introgressive Hybridization ◽  
White Oak ◽  
Gene Migration ◽  
The North ◽  
Geographic Structure ◽  
Phylogenetic Studies ◽  
Phylogenetic Informativeness ◽  
Lineage Divergence

Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11%–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30%–41% of plastome variation, geography 3%–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastome data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades.

scholarly journals Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Kevin P. Drees ◽  
Jeffrey M. Lorch ◽  
Sebastien J. Puechmaille ◽  
Katy L. Parise ◽  
Gudrun Wibbelt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
North American ◽  
Fungal Pathogen ◽  
Phylogenetic Study ◽  
Pseudogymnoascus Destructans ◽  
Long Distance ◽  
Recent Introduction ◽  
White Nose Syndrome ◽  
The North

ABSTRACT Globalization has facilitated the worldwide movement and introduction of pathogens, but epizoological reconstructions of these invasions are often hindered by limited sampling and insufficient genetic resolution among isolates. Pseudogymnoascus destructans , a fungal pathogen causing the epizootic of white-nose syndrome in North American bats, has exhibited few genetic polymorphisms in previous studies, presenting challenges for both epizoological tracking of the spread of this fungus and for determining its evolutionary history. We used single nucleotide polymorphisms (SNPs) from whole-genome sequencing and microsatellites to construct high-resolution phylogenies of P. destructans . Shallow genetic diversity and the lack of geographic structuring among North American isolates support a recent introduction followed by expansion via clonal reproduction across the epizootic zone. Moreover, the genetic relationships of isolates within North America suggest widespread mixing and long-distance movement of the fungus. Genetic diversity among isolates of P. destructans from Europe was substantially higher than in those from North America. However, genetic distance between the North American isolates and any given European isolate was similar to the distance between the individual European isolates. In contrast, the isolates we examined from Asia were highly divergent from both European and North American isolates. Although the definitive source for introduction of the North American population has not been conclusively identified, our data support the origin of the North American invasion by P. destructans from Europe rather than Asia. IMPORTANCE This phylogenetic study of the bat white-nose syndrome agent, P. destructans , uses genomics to elucidate evolutionary relationships among populations of the fungal pathogen to understand the epizoology of this biological invasion. We analyze hypervariable and abundant genetic characters (microsatellites and genomic SNPs, respectively) to reveal previously uncharacterized diversity among populations of the pathogen from North America and Eurasia. We present new evidence supporting recent introduction of the fungus to North America from a diverse Eurasian population, with limited increase in genetic variation in North America since that introduction.

scholarly journals Taxonomic and phylogenetic review of Necrosuchus ionensis (Alligatoroidea: Caimaninae) and the early evolution and radiation of caimanines

2019 ◽  
Vol 189 (2) ◽  
pp. 657-669 ◽  
Author(s):  
Giovanne M Cidade ◽  
Daniel Fortier ◽  
Annie S Hsiou
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
North American ◽  
Early Evolution ◽  
Valid Species ◽  
The North ◽  
Phylogenetic Studies ◽  
First Time ◽  
Salamanca Formation

Abstract Alligatoroidea is the most species-rich crocodylomorph clade of the Cenozoic of South America, with nearly all species belonging to the Caimaninae clade. However, the earliest records of Caimaninae in South America, which are from the Palaeocene, are based mostly on incomplete specimens, which increases the importance of detailed taxonomic and phylogenetic studies on these taxa. This paper offers a taxonomic and phylogenetic review of Necrosuchus ionensis, a caimanine species from the Salamanca Formation of the Palaeocene of Argentina. Necrosuchus ionensis is considered a valid species, albeit with a different diagnosis from that proposed by previous authors. The phylogenetic analysis shows, for the first time, that N. ionensis belongs to the derived Caimaninae clade Jacarea. However, a better understanding of the Jacarea clade is needed, and alternative placements for N. ionensis might be considered. Nevertheless, the placement of N. ionensis as a derived caimanine raises interesting perspectives on the early evolution and radiation of caimanines, which are thoroughly discussed in this paper together with other results obtained in this study, such as the recovery of the North American caimanines Bottosaurus and Tsoabichi as a clade.

scholarly journals (Lack of) Genetic Diversity in Immune Genes Predates Glacial Isolation in the North American Mountain Goat (Oreamnos americanus)

2012 ◽  
Vol 103 (3) ◽  
pp. 371-379 ◽  
Author(s):  
A. B. A. Shafer ◽  
C. W. Fan ◽  
S. D. Cote ◽  
D. W. Coltman
Keyword(s):  
Genetic Diversity ◽  
North American ◽  
Oreamnos Americanus ◽  
Immune Genes ◽  
The North ◽  
Mountain Goat

scholarly journals Genetic Diversity and Background Linkage Disequilibrium in the North American Holstein Cattle Population

2003 ◽  
Vol 86 (12) ◽  
pp. 4137-4147 ◽  
Author(s):  
R.L. Vallejo ◽  
Y.L. Li ◽  
G.W. Rogers ◽  
M.S. Ashwell
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
North American ◽  
Holstein Cattle ◽  
Cattle Population ◽  
The North

scholarly journals Genetic Diversity among Witchhazel Cultivars Based on Randomly Amplified Polymorphic DNA Markers

1997 ◽  
Vol 122 (4) ◽  
pp. 529-535 ◽  
Author(s):  
Robert D. Marquard ◽  
Eric P. Davis ◽  
Emily L. Stowe
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
North American ◽  
Dna Markers ◽  
Rapd Markers ◽  
North American Species ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
The North ◽  
Sib Families

Forty selections, including 37 cultivars of Hamamelis spp., were evaluated for genetic similarities using randomly amplified polymorphic DNA (RAPD) markers. Cluster analysis identified seven groups, which included three groups of H. ×intermedia cultivars, two groups of H. vernalis, and one group each of H. mollis and H. japonica. Three H. ×intermedia cultivars, `Arnold Promise', `Westerstede', and `Carmine Red', did not group closely with the other 20 cultivars of H. ×intermedia. Selections of the North American species H. vernalis were quite distinct from the Asiatic selections. However, data are presented that suggest hybridization exist between Asiatic Hamamelis spp. and H. vernalis. Genetic similarities between known half-sib families provides evidence that the cultivar pairs `Arnold Promise'—`Winter Beauty' and `Carmine Red'—`Hiltingbury' are, themselves, not likely half-sibs.

scholarly journals Improving phylogenetic resolution of the Lamiales using the complete plastome sequences of six Penstemon species

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261143
Author(s):  
Jason M. Stettler ◽  
Mikel R. Stevens ◽  
Lindsey M. Meservey ◽  
W. Wesley Crump ◽  
Jed D. Grow ◽  
...  
Keyword(s):  
North American ◽  
Central American ◽  
The Arctic ◽  
Temperate Grasslands ◽  
Individual Gene ◽  
The North ◽  
Phylogenetic Studies ◽  
Plastid Genomes ◽  
Evolutionary Radiation ◽  
Phylogenetic Resolution

The North American endemic genus Penstemon (Mitchell) has a recent geologic origin of ca. 3.6 million years ago (MYA) during the Pliocene/Pleistocene transition and has undergone a rapid adaptive evolutionary radiation with ca. 285 species of perennial forbs and sub-shrubs. Penstemon is divided into six subgenera occupying all North American habitats including the Arctic tundra, Central American tropical forests, alpine meadows, arid deserts, and temperate grasslands. Due to the rapid rate of diversification and speciation, previous phylogenetic studies using individual and concatenated chloroplast sequences have failed to resolve many polytomic clades. We investigated the efficacy of utilizing the plastid genomes (plastomes) of 29 species in the Lamiales order, including five newly sequenced Penstemon plastomes, for analyzing phylogenetic relationships and resolving problematic clades. We compared whole-plastome based phylogenies to phylogenies based on individual gene sequences (matK, ndhF, psaA, psbA, rbcL, rpoC2, and rps2) and concatenated sequences. We also We found that our whole-plastome based phylogeny had higher nodal support than all other phylogenies, which suggests that it provides greater accuracy in describing the hierarchal relationships among taxa as compared to other methods. We found that the genus Penstemon forms a monophyletic clade sister to, but separate from, the Old World taxa of the Plantaginaceae family included in our study. Our whole-plastome based phylogeny also supports the rearrangement of the Scrophulariaceae family and improves resolution of major clades and genera of the Lamiales.

scholarly journals Strong Genetic Differentiation Between North American and European Populations of Phytophthora alni subsp. uniformis

2013 ◽  
Vol 103 (2) ◽  
pp. 190-199 ◽  
Author(s):  
Jaime Aguayo ◽  
Gerard C. Adams ◽  
Fabien Halkett ◽  
Mursel Catal ◽  
Claude Husson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Mating System ◽  
North American ◽  
Parental Species ◽  
European Countries ◽  
North American Population ◽  
Natural Ecosystems ◽  
Reproduction Mode ◽  
The North

Alder decline caused by Phytophthora alni has been one of the most important diseases of natural ecosystems in Europe during the last 20 years. The emergence of P. alni subsp. alni —the pathogen responsible for the epidemic—is linked to an interspecific hybridization event between two parental species: P. alni subsp. multiformis and P. alni subsp. uniformis. One of the parental species, P. alni subsp. uniformis, has been isolated in several European countries and, recently, in North America. The objective of this work was to assess the level of genetic diversity, the population genetic structure, and the putative reproduction mode and mating system of P. alni subsp. uniformis. Five new polymorphic microsatellite markers were used to contrast both geographical populations. The study comprised 71 isolates of P. alni subsp. uniformis collected from eight European countries and 10 locations in North America. Our results revealed strong differences between continental populations (Fst = 0.88; Rst = 0.74), with no evidence for gene flow. European isolates showed extremely low genetic diversity compared with the North American collection. Selfing appears to be the predominant mating system in both continental collections. The results suggest that the European P. alni subsp. uniformis population is most likely alien and derives from the introduction of a few individuals, whereas the North American population probably is an indigenous population.

Loss of genetic diversity in the North American mayfly Ephemerella invaria associated with deforestation of headwater streams

2011 ◽  
Vol 56 (7) ◽  
pp. 1456-1467 ◽  
Author(s):  
LAURIE C. ALEXANDER ◽  
DAVID J. HAWTHORNE ◽  
MARGARET A. PALMER ◽  
WILLIAM O. LAMP
Keyword(s):  
Genetic Diversity ◽  
North American ◽  
Headwater Streams ◽  
The North ◽  
Loss Of Genetic Diversity
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