Analysis of diversity of natural populations and commercial lines of Echinacea using AFLP

An analysis of diversity of Echinacea native to North America, using amplified fragment length polymorphism (AFLP®), was carried out to complement a previously undertaken taxonomic revision of Echinacea that employed multivariate morphometrics. A total of 53 940 AFLP fragments, of which 40 455 were polymorphic, were scored on 435 individual plants from 58 populations consisting of ±10 individuals per population. The resulting polymorphism was sufficient to distinguish each plant. A monomorphic AFLP band and a polymorphic AFLP band that migrated at the same position, taken from samples of four species and eight varieties, were cloned, and multiple clones were sequenced. The polymorphic band at the same position across fragments was not identical, with identity as low as 23% compared with 50% identity of the monomorphic band, both of which were at the 100% threshold of sequence similarity. Thus, the AFLP banding profiles, irrespective of their sequence identity, were treated as phenotypes for population genetic, discriminant, and phylogenetic analyses. Variance components within populations and among populations within species were of equal magnitude, but the partitioned variation was slightly higher among varieties than among populations within varieties. Since no species-specific or variety-specific AFLP fingerprints were found, canonical discriminant analysis was conducted, resulting in support for four species but not for the varieties. Similar results were obtained with cluster and principal coordinate analyses, based on genetic distances. To achieve identification using AFLP fingerprints, various classificatory analyses were performed, followed by bootstrapping for validation. An example to identify an unknown plant at the species level with a minimum of 10 AFLP fragments, with greater than 82% overall correct classification, is provided. Phylogenetic analysis of all 435 individuals supported only Echinacea purpurea (L.) Moench and Echinacea laevigata (C.L. Boynton & Beadle) as separate entities, and only the three Echinacea atrorubens varieties and Echinacea pallida var. tennesseensis (Beadle) Binns, B.R. Baum & Arnason.Key words: Echinacea, population genetic analysis, multivariate analysis, AFLP band homologies.

Download Full-text

New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler)

Bulletin of Entomological Research ◽

10.1017/s000748531700116x ◽

2017 ◽

Vol 108 (5) ◽

pp. 636-644 ◽

Cited By ~ 3

Author(s):

W.-C. Zhu ◽

J.-T. Sun ◽

J. Dai ◽

J.-R. Huang ◽

L. Chen ◽

...

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

Natural Populations ◽

Source Area ◽

Population Genetic Analysis ◽

Outbreak Area ◽

Lepidoptera Noctuidae

AbstractAthetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

Download Full-text

A morphometric and molecular phylogenetic analysis of the African orchid genus Stenoglottis (Orchidaceae: Orchidoideae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa018 ◽

2020 ◽

Vol 193 (3) ◽

pp. 340-362 ◽

Cited By ~ 1

Author(s):

Dean P Phillips ◽

Benny Bytebier

Keyword(s):

Sequence Variation ◽

Phylogenetic Analyses ◽

Taxonomic Revision ◽

Plastid Dna ◽

Species Level ◽

Multivariate Morphometrics ◽

Species Boundaries ◽

Nuclear Markers ◽

Molecular Phylogenetic ◽

Small Genus

Abstract Stenoglottis is a small genus of forest orchids endemic to continental Africa. Nine taxa have so far been described, but species boundaries in the genus are problematic and several of these taxa are not widely accepted. In this study, taxon boundaries were investigated by means of a combination of morphometric and phylogenetic analyses, with the aim of resolving species-level relationships and identifying practical diagnostic characters. Sequence variation was low, particularly in plastid DNA (atpI-atpH), and Bayesian inference and maximum likelihood analyses of nuclear markers (ITS and ETS) did not resolve all of the putative taxa. Multivariate morphometrics (PCA, PCoA, cluster analysis) likewise did not support the recognition of all described Stenoglottis taxa, but they reliably distinguished some taxa that DNA data did not. Combined morphological and phylogenetic evidence supports the delimitation of five species and two varieties, for which characteristics of floral spurs, labella, leaves, bracts and auricles provide reliable diagnostic traits. These findings will form the basis of a taxonomic revision in which the proposed changes will be formalized.

Download Full-text

Pan-genome and phylogeny of Bacillus cereus sensu lato

10.1101/119420 ◽

2017 ◽

Cited By ~ 2

Author(s):

Adam L. Bazinet

Keyword(s):

Genetic Analysis ◽

Bacillus Cereus ◽

Population Genetic ◽

Phylogenetic Analyses ◽

Population Genetic Analysis ◽

Phylogenetic Clustering ◽

Pan Genome ◽

Gwas Analysis ◽

Reduced Representations ◽

Bacillus Cereus Sensu Lato

AbstractBackgroundBacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., “pan-GWAS” analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.MethodsA rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.The B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are “core” (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.

Download Full-text

Telomere length varies substantially between blood cell types in a reptile

Royal Society Open Science ◽

10.1098/rsos.192136 ◽

2020 ◽

Vol 7 (6) ◽

pp. 192136 ◽

Cited By ~ 3

Author(s):

Mats Olsson ◽

Nicholas J. Geraghty ◽

Erik Wapstra ◽

Mark Wilson

Keyword(s):

Blood Cell ◽

Telomere Length ◽

Whole Blood ◽

Phylogenetic Analyses ◽

Natural Populations ◽

Cell Types ◽

Tissue Type ◽

Telomeric Dna ◽

Blood Cell Type ◽

Widespread Phenomenon

Telomeres are repeat sequences of non-coding DNA-protein molecules that cap or intersperse metazoan chromosomes. Interest in telomeres has increased exponentially in recent years, to now include their ongoing dynamics and evolution within natural populations where individuals vary in telomere attributes. Phylogenetic analyses show profound differences in telomere length across non-model taxa. However, telomeres may also differ in length within individuals and between tissues. The latter becomes a potential source of error when researchers use different tissues for extracting DNA for telomere analysis and scientific inference. A commonly used tissue type for assessing telomere length is blood, a tissue that itself varies in terms of nuclear content among taxa, in particular to what degree their thrombocytes and red blood cells (RBCs) contain nuclei or not. Specifically, when RBCs lack nuclei, leucocytes become the main source of telomeric DNA. RBCs and leucocytes differ in lifespan and how long they have been exposed to ‘senescence' and erosion effects. We report on a study in which cells in whole blood from individual Australian painted dragon lizards ( Ctenophorus pictus ) were identified using flow cytometry and their telomere length simultaneously measured. Lymphocyte telomeres were on average 270% longer than RBC telomeres, and in azurophils (a reptilian monocyte), telomeres were more than 388% longer than those in RBCs. If this variation in telomere length among different blood cell types is a widespread phenomenon, and DNA for comparative telomere analyses are sourced from whole blood, evolutionary inference of telomere traits among taxa may be seriously complicated by the blood cell type comprising the main source of DNA.

Download Full-text

Adaptive Evolution of Relish, a Drosophila NF-κB/IκB Protein

Genetics ◽

10.1093/genetics/154.3.1231 ◽

2000 ◽

Vol 154 (3) ◽

pp. 1231-1238 ◽

Cited By ~ 1

Author(s):

David J Begun ◽

Penn Whitley

Keyword(s):

Immune Response ◽

Innate Immunity ◽

Genetic Analysis ◽

Adaptive Evolution ◽

Strong Evidence ◽

Population Genetic ◽

Microbial Pathogens ◽

Population Genetic Analysis ◽

Evolutionary Conflict ◽

A Site

Abstract NF-κB and IκB proteins have central roles in regulation of inflammation and innate immunity in mammals. Homologues of these proteins also play an important role in regulation of the Drosophila immune response. Here we present a molecular population genetic analysis of Relish, a Drosophila NF-κB/IκB protein, in Drosophila simulans and D. melanogaster. We find strong evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster. The adaptive evolution appears to be restricted to the IκB domain. A possible explanation for these results is that Relish is a site of evolutionary conflict between flies and their microbial pathogens.

Download Full-text

Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

Plant Systematics and Evolution ◽

10.1007/s00606-020-01730-3 ◽

2021 ◽

Vol 307 (2) ◽

Author(s):

Pau Carnicero ◽

Núria Garcia-Jacas ◽

Llorenç Sáez ◽

Theophanis Constantinidis ◽

Mercè Galbany-Casals

Keyword(s):

Eastern Mediterranean ◽

Phylogenetic Analyses ◽

Taxonomic Revision ◽

Distribution Patterns ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Long Distance ◽

Aegean Islands ◽

Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Download Full-text

Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.018754-0 ◽

2010 ◽

Vol 60 (11) ◽

pp. 2535-2539 ◽

Cited By ~ 36

Author(s):

Hui-Rong Li ◽

Yong Yu ◽

Wei Luo ◽

Yin-Xin Zeng

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Intertidal Sediment ◽

Rrna Gene ◽

Optimum Growth ◽

Temperature Range ◽

Zhongshan Station ◽

Diamino Acid ◽

Ph Range ◽

The Antarctic

Strain ZS314T was isolated from a sandy intertidal sediment sample collected from the coastal area off the Chinese Antarctic Zhongshan Station, east Antarctica (6 ° 22′ 13″ S 7 ° 21′ 41″ E). The cells were Gram-positive, motile, short rods. The temperature range for growth was 0–26 °C and the pH for growth ranged from 5 to 10, with optimum growth occurring within the temperature range 18–23 °C and pH range 6.0–8.0. Growth occurred in the presence of 0–6 % (w/v) NaCl, with optimum growth occurring in the presence of 2–4 % (w/v) NaCl. Strain ZS314T had MK-10 as the major menaquinone and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major fatty acids. The cell-wall peptidoglycan type was B2β with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content was approximately 67 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain ZS314T represents a new lineage in the family Microbacteriaceae. On the basis of the phylogenetic analyses and phenotypic characteristics, a new genus, namely Marisediminicola gen. nov., is proposed, harbouring the novel species Marisediminicola antarctica sp. nov. with the type strain ZS314T (=DSM 22350T =CCTCC AB 209077T).

Download Full-text

Evolutionary dynamics of spore killers.

Genetics ◽

10.1093/genetics/135.3.923 ◽

1993 ◽

Vol 135 (3) ◽

pp. 923-930 ◽

Cited By ~ 3

Author(s):

M J Nauta ◽

R F Hoekstra

Keyword(s):

Life Cycle ◽

Segregation Distortion ◽

Population Genetic ◽

Field Data ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Additional Advantage ◽

Genetic Modeling ◽

Spore Killing ◽

Ascospore Formation

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

Download Full-text