scholarly journals Genome-Wide Sequence-Based Genotyping Supports a Nonhybrid Origin of Castanea alabamensis

2021 ◽  
Vol 46 (4) ◽  
pp. 973-984
Author(s):  
M. Taylor Perkins ◽  
Tetyana Zhebentyayeva ◽  
Paul H. Sisco ◽  
J. Hill Craddock
Keyword(s):  
North American ◽  
Distinct Group ◽  
Morphological Diversity ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Eastern United States ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Conservation Concern

Abstract— The genus Castanea in North America contains several tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at > 100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

scholarly journals Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

2019 ◽  
Author(s):  
M. Taylor Perkins ◽  
Tetyana Zhebentyayeva ◽  
Paul H. Sisco ◽  
J. Hill Craddock
Keyword(s):  
North American ◽  
Distinct Group ◽  
Morphological Diversity ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Eastern United States ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Conservation Concern

AbstractThe genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Verification of Extratropical Cyclones within the NCEP Operational Models. Part I: Analysis Errors and Short-Term NAM and GFS Forecasts

2009 ◽  
Vol 24 (5) ◽  
pp. 1173-1190 ◽  
Author(s):  
Michael E. Charles ◽  
Brian A. Colle
Keyword(s):  
United States ◽  
North America ◽  
North American ◽  
Eastern Pacific ◽  
Extratropical Cyclones ◽  
Global Forecast System ◽  
Eastern United States ◽  
Forecast System ◽  
Short Term ◽  
The North

Abstract This paper verifies extratropical cyclones around North America and the adjacent oceans within the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS) and North American Mesoscale (NAM) models during the 2002–07 cool seasons (October–March). The analyzed cyclones in the Global Forecast System (GFS) model, North American Mesoscale (NAM) model, and the North American Regional Reanalysis (NARR) were also compared against sea level pressure (SLP) observations around extratropical cyclones. The GFS analysis of SLP was clearly superior to the NAM and NARR analyses. The analyzed cyclone pressures in the NAM improved in 2006–07 when its data assimilation was switched to the Gridpoint Statistical Interpolation (GSI). The NCEP GFS has more skillful cyclone intensity and position forecasts than the NAM over the continental United States and adjacent oceans, especially over the eastern Pacific, where the NAM has a large positive (underdeepening) bias in cyclone central pressure. For the short-term (0–60 h) forecasts, the GFS and NAM cyclone errors over the eastern Pacific are larger than the other regions to the east. There are relatively large biases in cyclone position for both models, which vary spatially around North America. The eastern Pacific has four to eight cyclone events per year on average, with errors >10 mb at hour 48 in the GFS; this number has not decreased in recent years. There has been little improvement in the 0–2-day cyclone forecasts during the past 5 yr over the eastern United States, while there has been a relatively large improvement in the cyclone pressure predictions over the eastern Pacific in the NAM.

A REVISION OF THE NORTH AMERICAN OMALIINAE (COLEOPTERA: STAPHYLINIDAE): THE GENERA ARPEDIUM ERICHSON AND EUCNECOSUM REITTER

1984 ◽  
Vol 116 (4) ◽  
pp. 487-527 ◽  
Author(s):  
J. M. Campbell
Keyword(s):  
United States ◽  
North American ◽  
Biological Data ◽  
Eastern United States ◽  
European Species ◽  
Boreal Species ◽  
Line Drawings ◽  
The North ◽  
New Synonymy ◽  
Scanning Electron

AbstractThe North American species of the genera Arpedium Erichson, and Eucnecosum Reitter are revised. Five species are recognized, the holarctic species E. brachypterum (Gravenhorst), E. tenue (LeConte) and E. brunnescens (J. Sahlberg), the transcontinental boreal species A. cribratum Fauvel and the eastern United States species A. schwarzi Fauvel.Lectotypes are designated for E. brachypterum, A. cribratum, A. angulare Fauvel (= A. cribratum), and A. schwarzi. The following new synonymy is established, Arpedium norvegicum var. sallasi Munster and Eucnecosum meybohmi Lohse (= E. tenue) and Arpedium angulare Fauvel and A. columbiense Hatch (= A. cribratum). All genera and species are described and illustrated with scanning electron photomicrographs and line drawings, four maps showing the North American distribution of each species are provided, and keys are presented to aid in the identification of all the species as well as the European species Arpedium quadrum (Gravenhorst). All available records and biological data for the species are summarized.The use of the generic name Eucnecosum Reitter is discussed and the transfer of brachypterum, tenue, and brunnescens from Arpedium to this genus by Lohse is confirmed.

A Field Key to the North American Species of Hylobius (Curculionidae)

1961 ◽  
Vol 93 (7) ◽  
pp. 501-502 ◽  
Author(s):  
R. J. Finnegan
Keyword(s):  
United States ◽  
North American ◽  
Economic Importance ◽  
North American Species ◽  
Eastern United States ◽  
Eastern Canada ◽  
The North

There are five known North American species in the genus Hylobius; H. pales (Hbst.), H. congener Dalla Torre, H. pinicola (Couper), H. radicis Buch., and H. warreni Wood. In recent years four of these species have increased considerably in economic importance in central and eastern Canada and the eastern United States; H. pales and H. radicis attacking pines and H. pinicola and H. warreni attacking spruces and pines. H. congener occurs only in small numbers and little is known about its ecology. It is important, therefore, to be able to separate these species readily in the field.

scholarly journals Interactions between natural selection and recombination shape the genomic landscape of introgression

2021 ◽  
Author(s):  
Maud Duranton ◽  
John Pool
Keyword(s):  
North American ◽  
African Ancestry ◽  
North American Population ◽  
Evolutionary Forces ◽  
The North ◽  
Genome Wide ◽  
Genomic Landscape ◽  
The One ◽  
The Relationship ◽  
Genomic Patterns

AbstractHybridization between lineages that have not reached complete reproductive isolation appears more and more like a common phenomenon. Indeed, speciation genomics studies have now extensively shown that many species’ genomes have hybrid ancestry. However, genomic patterns of introgression are often heterogeneous across the genome. In many organisms, a positive correlation between introgression levels and recombination rate has been observed. It is usually explained by the purging of deleterious introgressed material due to incompatibilities. However, the opposite relationship was observed in a North American population of Drosophila melanogaster with admixed European and African ancestry. In order to explore how directional and epistatic selection can impact the relationship between introgression and recombination, we performed forward simulations of whole D. melanogaster genomes reflecting the North American population’s history. Our results revealed that the simplest models of positive selection often yield negative correlations between introgression and recombination such as the one observed in D. melanogaster. We also confirmed that incompatibilities tend to produce positive introgression-recombination correlations. And yet, we identify parameter space under each model where the predicted correlation is reversed. These findings deepen our understanding of the evolutionary forces that may shape patterns of ancestry across genomes, and they strengthen the foundation for future studies aimed at estimating genome-wide parameters of selection in admixed populations.

Platanthera lacera × leucophaea, a new cryptic natural hybrid, and a key to northeastern North American fringed-orchids

1999 ◽  
Vol 77 (8) ◽  
pp. 1144-1149 ◽  
Author(s):  
Paul M Catling ◽  
Vivian R Brownell
Keyword(s):  
North American ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Herbarium Specimens ◽  
Morphological Attributes ◽  
Quantitative Characters ◽  
Hybrid Plants ◽  
York County ◽  
Spur Length ◽  
Platanthera Leucophaea

To evaluate the putative hybrid origin of fringed-orchids from York County, Ontario, morphological attributes of hybrid flowers were evaluated with respect to both a random sample of herbarium specimens and populations from the hybrid location. The putative hybrids were intermediate in spur length, petal width, and vertical distance across opening to the spur as well as in eight other quantitative characters. The hybrid is named Platanthera ×hollandiae Catling & Brownell (= Platanthera lacera (Michx.) G. Don × Platanthera leucophaea (Nutt.) Lindl.). With pale greenish-white flowers, partly reflexed lateral sepals, and a horizontally linear spur opening, the putative hybrid plants resemble P. lacera but can be readily distinguished by their relatively long spurs, relatively broad lateral petals, and ovoid instead of strap-shaped viscidium. A key including characteristics of the column is included that allows the separation of all northeastern North American fringed-orchids and their known natural hybrids.Key words: orchid, hybrid, Platanthera lacera, Platanthera leucophaea, Canada, Ontario.

scholarly journals The genetic prehistory of the Greater Caucasus

2018 ◽  
Author(s):  
Chuan-Chao Wang ◽  
Sabine Reinhold ◽  
Alexey Kalmykov ◽  
Antje Wissgott ◽  
Guido Brandt ◽  
...  
Keyword(s):  
Native American ◽  
Human Movement ◽  
North Caucasus ◽  
Hunter Gatherers ◽  
The Caucasus ◽  
The North ◽  
European Languages ◽  
Snp Data ◽  
Genome Wide ◽  
Show Evidence

AbstractArchaeogenetic studies have described the formation of Eurasian ‘steppe ancestry’ as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4thmillennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that – unlike today – the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.

scholarly journals Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae)

2019 ◽  
Author(s):  
Alexey Shipunov ◽  
Sofia Gladkova ◽  
Polina Timoshina ◽  
Hye Ji Lee ◽  
Jinhee Choi ◽  
...  
Keyword(s):  
North American ◽  
Morphological Diversity ◽  
Molecular Data ◽  
North American Species ◽  
Hybrid Origin ◽  
Species Boundaries ◽  
Molecular Analyses ◽  
European Species ◽  
Generic Hybrid ◽  
Woody Shrubs

Aronia Medik. (chokeberry, Rosaceae) is a genus of woody shrubs with two or three North American species. Species boundaries and relationships between species of Aronia are frequently under question. The only European species in the genus, A. mitschurinii A.K.Skvortsov & Maitul., is suggested to be an inter-generic hybrid. In order to clarify the relationships between species of Aronia, we performed several morphometric and molecular analyses and found that the molecular and morphological diversity within data on American Aronia is low, and species boundaries are mostly not clearly expressed. Whereas morphology is able to separate American species from A. mitschurinii, there is no support for such discrimination from the molecular data; our analyses did not reveal evidence of A. mitschurinii hybrid origin. We believe that higher-resolution markers are needed to resolve species boundaries and putative hybridization events.

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