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.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 62 (1) ◽  
pp. 427-446 ◽  
Author(s):  
Susana Schönhuth ◽  
David M. Hillis ◽  
David A. Neely ◽  
Lourdes Lozano-Vilano ◽  
Anabel Perdices ◽  
...  
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
The North

scholarly journals First Report of Heterobasidion annosum on the Endemic Abies hickeli of Southern Mexico

Plant Disease ◽  
2000 ◽  
Vol 84 (9) ◽  
pp. 1047-1047 ◽  
Author(s):  
M. Garbelotto ◽  
I. Chapela
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Heterobasidion Annosum ◽  
Internal Transcribed Spacer Region ◽  
Southern Mexico ◽  
Geographic Ranges ◽  
The North ◽  
Mexican State ◽  
Standing Trees ◽  
Pinus Spp

The basidiomycete Heterobasidion annosum (Fr.:Fr.) Bref. is a pathogen of conifers in the Northern Hemisphere. This fungus has been previously reported from Pinus spp. (1) and from Abies religiosa (H.B.K.) Schl. et Cham. (2) in Central Mexico. In 1998, H. annosum was collected for the first time from stumps of Abies hickeli Flous et Gaussen in the Southern Mexican State of Oaxaca, at an altitude of 2,900 m (Lat 17° 28′ N, Long 96° 31′ W). Although standing trees at the sampled site were asymptomatic, the sapwood and heartwood of several fir stumps were extensively decayed. The white laminated rot was similar to that caused by H. annosum on other Abies spp. Decay pockets extended to the upper surface of the stumps, indicating the fungus had infected and colonized the tree butts prior to tree felling. H. annosum basidiocarps were found both outside the roots in the duff layer and inside the decay pockets. The anamorph of H. annosum (Spiniger meineckellum (A. Olson) Stalpers) was isolated from the context of three basidiocarps. Based on comparative analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer region, all three isolates belonged to the North American S intersterility group (ISG). This report expands the host and the geographic ranges of the North American S ISG, and represents the world's southernmost finding of an Abies species infected by this pathogen. References: (1) R. Martinez Barrera and R. Sanchez Ramirez. Ciencia Forestal 5(26):3, 1980. (2) M. Ruiz-Rodriguez and L. M. Pinzon-Picaseno. Bol. Soc. Bot. Mexico 54:225, 1994.

Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 1039-1064 ◽  
Author(s):  
Stephen R. Downie ◽  
Deborah S. Katz-Downie ◽  
Feng-Jie Sun ◽  
Chang-Shook Lee
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Intergenic Spacers ◽  
Rdna Its ◽  
The North

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

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 North American Tropical Cyclone Landfall and SST: A Statistical Model Study

2013 ◽  
Vol 26 (21) ◽  
pp. 8422-8439 ◽  
Author(s):  
Timothy Hall ◽  
Emmi Yonekura
Keyword(s):  
North Atlantic ◽  
North American ◽  
The North ◽  
Geographic Structure ◽  
Model Study ◽  
Complete Life Cycle ◽  
Hurricane Season ◽  
Major Hurricane ◽  
And Shifts ◽  
The Relationship

Abstract A statistical–stochastic model of the complete life cycle of North Atlantic (NA) tropical cyclones (TCs) is used to examine the relationship between climate and landfall rates along the North American Atlantic and Gulf Coasts. The model draws on archived data of TCs throughout the North Atlantic to estimate landfall rates at high geographic resolution as a function of the ENSO state and one of two different measures of sea surface temperature (SST): 1) SST averaged over the NA subtropics and the hurricane season and 2) this SST relative to the seasonal global subtropical mean SST (termed relSST). Here, the authors focus on SST by holding ENSO to a neutral state. Jackknife uncertainty tests are employed to test the significance of SST and relSST landfall relationships. There are more TC and major hurricane landfalls overall in warm years than cold, using either SST or relSST, primarily due to a basinwide increase in the number of storms. The signal along the coast, however, is complex. Some regions have large and significant sensitivity (e.g., an approximate doubling of annual major hurricane landfall probability on Texas from −2 to +2 standard deviations in relSST), while other regions have no significant sensitivity (e.g., the U.S. mid-Atlantic and Northeast coasts). This geographic structure is due to both shifts in the regions of primary TC genesis and shifts in TC propagation.

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.

Contrasting demographic histories of European and North American sea lamprey (Petromyzon marinus) populations inferred from mitochondrial DNA sequence variation

2012 ◽  
Vol 63 (9) ◽  
pp. 827 ◽  
Author(s):  
Martin J. Genner ◽  
Robert Hillman ◽  
Matthew McHugh ◽  
Stephen J. Hawkins ◽  
Martyn C. Lucas
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
North American ◽  
Petromyzon Marinus ◽  
Population Expansion ◽  
Sea Lamprey ◽  
European Population ◽  
North American Population ◽  
American Population ◽  
The North

Populations of anadromous sea lamprey (Petromyzon marinus) have been found to be largely genetically homogeneous across western Europe, and across the eastern seaboard of North America. However, comparatively little is known of the relationship between the European and North American populations. We quantified the extent of population structuring present over a transatlantic scale using mitochondrial DNA sequences. We found clear segregation of the populations on either side of the Atlantic, and considerable genetic homogeneity within Europe over a spatial scale of over 2000 km. The North American populations contained larger genetic diversity than those from Europe, and coalescent analyses showed a corresponding greater overall effective population size. Employing calibration points based on a dated phylogeny of the Petromyzontiformes, our analyses indicated that the North American population has been increasing in effective size since establishment ~500 000 years ago, while the total European population has only undergone population expansion only within the last 125 000 years. This evidence is consistent with a colonisation of Europe from an older North American population, and with the European population persisting through the last glaciation within regional refugia.

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