Reply to the comment by Salamini et al. on "AFLP data and the origins of domesticated crops"

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 621-622 ◽  
Author(s):  
Robin G Allaby ◽  
Terence A Brown
Keyword(s):  
Tetraploid Wheat ◽  
Neighbor Joining ◽  
Crop Domestication ◽  
Critical Question ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Tetraploid Wheats ◽  
Key Points

We reiterate the key points of a previous paper that showed that neighbor-joining analysis of AFLP datasets can produce erroneous results. The critical question, whether the datasets used to infer the origins of einkorn, barley, and the hulled and hard tetraploid wheats display sufficient linkage to avoid the artifacts that we observed, is not adequately answered by Salamini et al.Key words: AFLPs, crop domestication, einkorn wheat, barley, tetraploid wheat.

scholarly journals Comment on "AFLP data and the origins of domesticated crops"

Genome ◽  
2004 ◽  
Vol 47 (3) ◽  
pp. 615-620 ◽  
Author(s):  
F Salamini ◽  
M Heun ◽  
A Brandolini ◽  
H Özkan ◽  
J Wunder
Keyword(s):  
Phylogenetic Tree ◽  
Dna Fingerprinting ◽  
Phylogenetic Analyses ◽  
Tetraploid Wheat ◽  
Aflp Markers ◽  
Crop Domestication ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Fertile Crescent ◽  
Tree Topologies

We review some concepts and methods of handling and using DNA fingerprinting in phylogenetic analyses related to crop domestication. Particular reference is made to AFLP markers and mode and place of einkorn, barley, and tetraploid wheat domestication in the Neolithic by human communities in the Fertile Crescent. The reconsideration of AFLP databases of domesticated and wild lines demonstrates that phylogenetic tree topologies, originally described for the three species, match closely the new results obtained by principle coordinate analyse.Key words: AFLPs, discontinuous markers, crop domestication, einkorn wheat, barley, tetraploid wheat.

AFLP data and the origins of domesticated crops

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 448-453 ◽  
Author(s):  
Robin G Allaby ◽  
Terence A Brown
Keyword(s):  
Population Biology ◽  
Fragment Length Polymorphism ◽  
Plant Domestication ◽  
Neighbor Joining ◽  
Cereal Crop ◽  
Einkorn Wheat ◽  
Aflp Data ◽  
Monophyletic Origin ◽  
Aflp Genotyping ◽  
Domestication Process

Amplified fragment length polymorphism (AFLP) datasets have been used to construct neighbor-joining trees from which monophyletic origins for crops such as einkorn wheat, barley, and emmer wheat have been inferred. We simulated several different multiple domestication scenarios for an imaginary cereal crop and examined the resulting domesticated populations. The simulations showed that the population biology aspects of the domestication process can result in independently domesticated populations merging in such a way that a monophyletic origin is erroneously inferred when the resulting population is examined by AFLP genotyping and neighbor-joining analysis. The results bring into question the use of this method to infer the origins of real crops.Key words: AFLPs, agriculture, neighbor-joining, plant domestication.

Genetic diversity of Echinacea species based upon amplified fragment length polymorphism markers

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 102-111 ◽  
Author(s):  
D -H Kim ◽  
D Heber ◽  
D W Still
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length ◽  
Echinacea Purpurea ◽  
Morphological Characters ◽  
Pairwise Distance ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Phenetic Relationships ◽  
Length Polymorphisms

The taxonomy of Echinacea is based on morphological characters and has varied depending on the monographer. The genus consists of either nine species and four varieties or four species and eight varieties. We have used amplified fragment length polymorphisms (AFLP) to assess genetic diversity and phenetic relationships among nine species and three varieties of Echinacea (sensu McGregor). A total of 1086 fragments, of which approximately 90% were polymorphic among Echinacea taxa, were generated from six primer combinations. Nei and Li's genetic distance coefficient and the neighbor-joining algorithm were employed to construct a phenetic tree. Genetic distance results indicate that all Echinacea species are closely related, and the average pairwise distance between populations was approximately three times the intrapopulation distances. The topology of the neighbor-joining tree strongly supports two major clades, one containing Echinacea purpurea, Echinacea sanguinea, and Echinacea simulata and the other containing the remainder of the Echinacea taxa (sensu McGregor). The species composition within the clades differs between our AFLP data and the morphometric treatment offered by Binns and colleagues. We also discuss the suitability of AFLP in determining phylogenetic relationships.Key words: Echinacea, AFLP, genetic distance, phylogeny.

Amplified fragment length polymorphism analysis reveals three distinct taxa in Carex digitalis sect. Careyanae (Cyperaceae)

2006 ◽  
Vol 84 (9) ◽  
pp. 1444-1452 ◽  
Author(s):  
Bruce A. Ford ◽  
Robert F.C. Naczi ◽  
Habibollah Ghazvini ◽  
Mahmood Iranpour
Keyword(s):  
North Carolina ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Polymorphism Analysis ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Additional Species ◽  
Pair Group

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis , var. floridana , var. macropoda ). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora.

Nucleolar competition analysis in Aegilops ventricosa and its amphiploids with tetraploid wheats and diploid rye by the silver-staining procedure

1984 ◽  
Vol 26 (1) ◽  
pp. 34-39 ◽  
Author(s):  
J. Orellana ◽  
J. L. Santos ◽  
J. R. Lacadena ◽  
M. C. Cermeño
Keyword(s):  
Secale Cereale ◽  
Silver Staining ◽  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Nucleolar Organizer ◽  
Triticum Dicoccoides ◽  
Staining Procedure ◽  
Nucleolar Organizer Regions ◽  
Aegilops Ventricosa ◽  
Tetraploid Wheats

The nucleolar organizer activity of Aegilops ventricosa and its amphiploids with tetraploid wheats (Triticum turgidum, Triticum dicoccum, and Triticum aethiopicum) and diploid rye (Secale cereale) was analyzed by the silver-staining procedure. Triticum turgidum and Triticum dicoccoides show four Ag-NORs (silver-stained nucleolar organizer regions), in agreement with previous data. Only two Ag-NORs are detected in Ae. ventricosa (genome constitution DDMM) indicating that natural amphiplasty occurs in this allotetraploid species. No amphiplasty was observed in the Ae. ventricosa – tetraploid wheat amphiploids since six Ag-NORs were visible in all of them. On the contrary, only two Ag-NORs were detected in the Ae. ventricosa – Secale cereale amphiploid, the rye NORs being suppressed by the presence of ventricosa chromosomes. The ventricosa NORs therefore are codominant with those of tetraploid wheat (chromosomes 1B and 6B) and dominant to chromosome 1R of rye. Eleven T. aestivum – Ae. ventricosa addition lines have been also analyzed. All of them showed four Ag-NORs. Clear-cut conclusions were not reached since the added ventricosa chromosomes were not identified.

Systematic relationships in Lathyrus sect. Lathyrus (Fabaceae) based on amplified fragment length polymorphism (AFLP) data

2002 ◽  
Vol 80 (9) ◽  
pp. 962-969 ◽  
Author(s):  
Abdelfattah Badr ◽  
Hanaa El Shazly ◽  
Haddad El Rabey ◽  
Linda E Watson
Keyword(s):  
Phylogenetic Tree ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Neighbor Joining ◽  
Aflp Data ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Close Relationship ◽  
Systematic Relationships

Amplified fragment length polymorphisms (AFLP) were utilized to examine systematic relationships in Lathyrus L. sect. Lathyrus (Fabaceae). In addition to a parsimony-based phylogenetic tree, AFLP-based trees were constructed using Dice, Jaccard, and mean character difference coefficients to produce distance-based trees using the UPGMA and neighbor-joining methods. All trees clearly show a close relationship among accessions of the same species, confirming the monophyly of the species examined. All analyses indicate that species of the section Lathyrus are distinct from species of other sections. These findings confirm the monophyly of the section and contradict proposals to split it. They do not support the segregation of L. gorgoni in the section Gorgonia. Within the section Lathyrus, several relationships are present but are only weakly supported. The use of AFLP data to resolve systematic relationships in the genus Lathyrus is further demonstrated.Key words: Lathyrus, Fabaceae, systematics, AFLP.

Aneuploid analyses of hybrid necrosis and hybrid chlorosis in tetraploid wheats using the D genome chromosome substitution lines of durum wheat

Genome ◽  
1992 ◽  
Vol 35 (4) ◽  
pp. 594-601 ◽  
Author(s):  
Koichiro Tsunewaki
Keyword(s):  
Durum Wheat ◽  
Tetraploid Wheat ◽  
Hybrid Necrosis ◽  
Chromosome Substitution ◽  
Substitution Lines ◽  
Genome Chromosome ◽  
D Genome ◽  
Chromosome Substitution Lines ◽  
Complementary Genes ◽  
Tetraploid Wheats

Chromosomal locations of the Ne1 gene, one of the two complementary genes for type 1 hybrid necrosis, and two complementary genes, Cs1 and Cs2, for type 2 hybrid chlorosis in tetraploid wheats were determined by aneuploid analyses employing the D genome chromosome substitution lines of 'Langdon' durum wheat. The Ne1 gene of 'Langdon' is located on chromosome 5B, whereas the Cs1 gene of Triticum dicoccum 'Hokudai' and the Cs2 gene of T. timopheevi are located on chromosomes 5A and 4G, respectively. Chromosomes 4B and 4G show almost complete functional compensation, though they rarely pair with each other, but chromosome 4D of T. aestivum 'Chinese Spring' has only half the ability of chromosome 4G in compensating for chromosome 4B on the fertilization ability of the male gamete. The results have demonstrated the usefulness of the D genome chromosome substitution lines of durum wheat for determining the chromosomes carrying major genes in tetraploid wheat. The results of these studies support the reallocation of chromosome 4A to the B genome.Key words: durum wheat, hybrid necrosis, hybrid chlorosis, aneuploid analyses, chromosome substitution lines.

scholarly journals Evolution of Homeologous Gene Expression in Polyploid Wheat

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1401
Author(s):  
Na Zhao ◽  
Qianli Dong ◽  
Brian D. Nadon ◽  
Xiaoyang Ding ◽  
Xutong Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary History ◽  
Tetraploid Wheat ◽  
Differentially Expressed ◽  
Functional Categories ◽  
Polyploid Wheat ◽  
Tetraploid Wheats ◽  
Regulatory Changes ◽  
History Of ◽  
Homeologous Gene

Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.

Autism and Neurodiversity: Addressing Concerns and Offering Implications for the School-Based Speech-Language Pathologist

2020 ◽  
pp. 1-7
Author(s):  
Laura S. DeThorne ◽  
Kelly Searsmith
Keyword(s):  
Service Provision ◽  
Individualized Education Program ◽  
Institutional Constraints ◽  
Individualized Education ◽  
Existing Structures ◽  
Eligibility Determination ◽  
Speech Language Pathologist ◽  
School Based ◽  
Key Points ◽  
C Center

Purpose The purpose of this article is to address some common concerns associated with the neurodiversity paradigm and to offer related implications for service provision to school-age autistic students. In particular, we highlight the need to (a) view first-person autistic perspectives as an integral component of evidence-based practice, (b) use the individualized education plan as a means to actively address environmental contributions to communicative competence, and (c) center intervention around respect for autistic sociality and self-expression. We support these points with cross-disciplinary scholarship and writings from autistic individuals. Conclusions We recognize that school-based speech-language pathologists are bound by institutional constraints, such as eligibility determination and Individualized Education Program processes that are not inherently consistent with the neurodiversity paradigm. Consequently, we offer examples for implementing the neurodiversity paradigm while working within these existing structures. In sum, this article addresses key points of tension related to the neurodiversity paradigm in a way that we hope will directly translate into improved service provision for autistic students. Supplemental Material https://doi.org/10.23641/asha.13345727

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