From Dampier to DNA: the 300-year-old mystery of the identity and proposed allopolyploid origin of Conostylis stylidioides (Haemodoraceae)

2001 ◽  
Vol 49 (5) ◽  
pp. 611 ◽  
Author(s):  
Siegfried L. Krauss ◽  
Stephen D. Hopper
Keyword(s):  
Genetic Variation ◽  
Maximum Parsimony ◽  
Hybrid Origin ◽  
Maximum Parsimony Tree ◽  
Aflp Data ◽  
Parsimony Tree ◽  
Different Populations ◽  
Current Species ◽  
Origin Hypothesis ◽  
Hybridisation Event

The tetraploid Conostylis stylidioides (n= 16) has been proposed to be a stabilised hybrid between the diploid (n = 8) species C. prolifera and C. candicans because of morphological and geographical intermediacy, as well as a polyploid chromosome number. To test this hybrid-origin hypothesis, we used the DNA-fingerprinting technique amplified fragment length polymorphism (AFLP) and measured genetic variation within these taxa, as well as the putative outgroups C. robusta and C. aculeata. One AFLP primer pair generated 192 dominant markers for 36 samples from these species, of which 189 were polymorphic. Polymorphism within populations was uniformly high for all species, with 66–86% of all fragments polymorphic and estimates of heterozygosity ranging from 0.36 to 0.41. Ordination, UPGMA and maximum parsimony analyses of these genetic data consistently clustered species, supporting the current species’ level taxonomy. The intermediate placement of C. stylidioides between C. proliferaand C. candicans on the maximum parsimony tree supports the hybrid-origin hypothesis, although other interpretations are possible. The phenetic results for AFLP data, in which C. stylidioides is not strictly intermediate between C. prolifera and C. candicans, are either concordant with recent research suggesting that rapid intra- and inter-genomic rearrangements occur with the origin of polyploid taxa, or indicate an ancient hybridisation event. While our results do not reject the hybrid origin hypothesis, the extremely high levels of genetic variation detected with AFLP within these populations, in combination with extensive genomic reorganisation with the origin of C. stylidioides and the possibility of independent origins for different populations, make it difficult to confidently exclude other scenarios.

Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

2018 ◽  
Vol 32 (2) ◽  
pp. 319 ◽  
Author(s):  
Xuankun Li ◽  
David K. Yeates
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Junior Synonym ◽  
Maximum Parsimony Tree ◽  
New Combinations ◽  
New Genera ◽  
Parsimony Tree

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E4A86A19-4AC3-498C-8BDF-B8B501E5A248

Corrigendum to: Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

2018 ◽  
Vol 32 (2) ◽  
pp. 504
Author(s):  
Xuankun Li ◽  
David K. Yeates
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Junior Synonym ◽  
Maximum Parsimony Tree ◽  
New Combinations ◽  
New Genera ◽  
Link Type ◽  
Parsimony Tree

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. <a ext-link-type=

scholarly journals MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Diep Thi Hoang ◽  
Le Sy Vinh ◽  
Tomáš Flouri ◽  
Alexandros Stamatakis ◽  
Arndt von Haeseler ◽  
...  
Keyword(s):  
Maximum Parsimony ◽  
Maximum Parsimony Tree ◽  
Bootstrap Approximation ◽  
Parsimony Tree ◽  
Tree Inference

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

ITS sequence variation supports the hybrid origin of Malus toringoides Hughes

2007 ◽  
Vol 85 (7) ◽  
pp. 659-666 ◽  
Author(s):  
Ting-Ting Feng ◽  
Zhi-Qin Zhou ◽  
Jian-Min Tang ◽  
Ming-Hao Cheng ◽  
Shi-Liang Zhou
Keyword(s):  
Sequence Variation ◽  
Gene Tree ◽  
Natural Populations ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Molecular Evidence ◽  
Sequence Information ◽  
Aflp Data

Malus toringoides (Rehd.) Hughes was suggested to have originated from hybridization between Malus transitoria Schneid. and Malus kansuensis Rehd., followed by repeated backcrossing to one of the putative parents. In the present study, the sequence information of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) was used to re-examine the origin of this species. A total of 69 accessions from three natural populations (Maerkang, Xiaba and Kehe, Aba Autonomous Region, Sichuan, China) of M. toringoides and 10 accessions of its putative parents were analyzed. Using Malus angustifolia (Ait.) Michx., Malus ioensis (Wood) Britt. and Malus doumeri Chev. as outgroups, our phylogenetic analysis of the ITS sequences of M. toringoides and its putative parents showed that M. toringoides was not monophyletic, and two different types of ITS sequences which were obtained from each of the six accessions of M. toringoides were found to have clustered separately with those of the two putative parent species on the gene tree. A comparison of the sequence variation between M. toringoides and its putative parents revealed an additive variation pattern of ITS sequences in the putative hybrid species. These results are consistent with the previous morphological and amplified fragment length polymorphism (AFLP) data which suggested that M. toringoides was of hybrid origin. Our ITS data provide new molecular evidence for the hybrid origin hypothesis of M. toringoides and these results are of great importance for future study on hybridization, polyploid speciation and evolution of the genus Malus Miller.

scholarly journals Genetic variations in the drug metabolizing enzyme, CYP2E1, among various ethnic populations of Pakistan

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9721
Author(s):  
Sagheer Ahmed ◽  
Nadeem Altaf ◽  
Mahnoor Ejaz ◽  
Zaira Zulfiqar ◽  
Kholood Janjua ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Adverse Effects ◽  
Drug Response ◽  
Variable Response ◽  
Healthy Human ◽  
Pakistani Population ◽  
Drug Metabolizing Enzyme ◽  
Different Populations ◽  
Metabolizing Enzyme ◽  
Low Activity

Genetic polymorphism in cytochrome P450 (CYP) monooxygenase genes is an important source of interindividual variability of drug response. CYP enzyme activities may change as a result of such polymorphisms which then, may affect drug metabolism. This would result in a change in the severity and frequency of adverse effects in addition to the non-responder phenomenon. CYP2E1, a member of CYP superfamily, affects the metabolism of several clinically important drugs such as halothane, paracetamol, etc. Genetic variation in CYP2E1 is known to cause significant inter-individual differences in drug response and adverse effects. The degree of genetic variation is found to be different in different populations around the world. The frequencies of two important polymorphisms in the CYP2E1*7C, NC_000010.10:g.135340548A>G (rs2070672) and CYP2E1, NC_000010.10:g.135339244G>C (rs3813865), are not known in the Pakistani population. In the present investigation, 636 healthy human volunteers were screened for these two single nucleotide polymorphism. Our results indicate that about 18% (rs2070672) and 28% (rs3813865) of the Pakistani population has a genotype containing at least one low activity allele. A significant interethnic variation in the frequencies of both the polymorphisms was observed. These results suggest that pharmacogenetics screening for low activity genotypes would be a helpful tool for clinicians when they prescribe medications metabolized by CYP2E1, as a significant fraction of the Pakistani population is expected to have a variable response to these drugs.

scholarly journals A phylogenetic analysis of the genus Pleurothallis, with emphasis on Pleurothallis subsection Macrophyllae-Fasciculatae, using nuclear ITS and chloroplast DNA sequencing

Lankesteriana ◽  
2011 ◽  
Vol 11 (3) ◽  
Author(s):  
M. Wilson ◽  
C. Belle ◽  
A. Dang ◽  
P. Hannan ◽  
C. Kenyon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Preliminary Data ◽  
Plastid Dna ◽  
Maximum Parsimony Tree ◽  
Its Sequencing ◽  
Phylogenetic Studies ◽  
Parsimony Tree ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Expanded Concept

Several revisions of the genus Pleurothallis have been proposed. Luer has proposed that Pleurothallis species in subgenus Scopula be segregated into the genera Colombiana and Ancipitia. Szlachetko and Margonska (2001) proposed the genus Zosterophyllanthos for Pleurothallis subsection Macrophyllae-Fasciculatae. As an alternative, Luer (2005) proposed the genus Acronia by uniting Pleurothallis subsection Macrophyllae-Fasciculatae with subsections Acroniae and Amphygiae. The molecular phylogenetic studies by Pridgeon and Chase (2001), however, suggested that these taxonomic revisions might not be justified. We report here a more detailed phylogenetic analysis of the genus Pleurothallis, with emphasis on subsection Macrophyllae-Fasciculatae, with data primarily from nuclear ITS sequencing, supplemented with preliminary data from plastid DNA (rpoB2, rpoC1, and ycf1) sequencing. Some initial, tentative conclusions can be drawn. In the strict consensus maximum-parsimony tree of ITS data, many of the clades collapse, leaving a polytomy with a single, highly supported node that tentatively could be used to delimit the genus Pleurothallis. Such a tree would argue for an expanded concept of the genus Pleurothallis, in which the groups Ancipitia, Colombiana, and Acronia/Zosterophyllanthos, if shown to be monophyletic, are relegated to subgenera. 

scholarly journals Reciprocal hybridization between diploid Ficaria calthifolia and tetraploid Ficaria verna subsp. verna: evidence from experimental crossing, genome size and molecular markers

2019 ◽  
Vol 189 (3) ◽  
pp. 293-310 ◽  
Author(s):  
Ondřej Popelka ◽  
Michal Sochor ◽  
Martin Duchoslav
Keyword(s):  
Genome Size ◽  
Morphological Variability ◽  
Plastid Dna ◽  
Genotypic Diversity ◽  
Hybrid Origin ◽  
Aflp Analysis ◽  
Sympatric Populations ◽  
Aflp Data ◽  
Evolutionary Forces ◽  
Genetic Clusters

Abstract Ficaria is a taxonomically intriguing polyploid complex with high morphological variability. Both hybridization and polyploidization have been suggested as the main evolutionary forces behind the high morphological variability in this genus; however, detailed studies are lacking. In Central Europe, two Ficaria taxa (diploid F. calthifolia and tetraploid F. verna subsp. verna) occasionally co-occur in local sympatry, which might result in hybridization. We investigated sympatric populations of the two Ficaria taxa using flow cytometry, chromosome counts, AFLP analysis and plastid DNA sequencing; we also performed experimental homoploid and heteroploid crosses to determine the frequency and direction of hybrid triploid formation, an alternative route of triploid origin (autopolyploidy) and the possibility of a one-step neoallotetraploid origin. Sympatric populations were composed of three genetic clusters corresponding to diploid F. calthifolia (2n = 16), tetraploid F. verna subsp. verna (2n = 32) and triploid plants (2n = 24). The holoploid genome size and AFLP data suggest a hybrid origin of the triploids, thereby making their formation via autopolyploidization in F. calthifolia unlikely. The triploid populations are monoclonal and of independent origin. In contrast, the parental populations exhibit high genotypic diversity and frequent sexual reproduction, including those of predominantly asexual F. verna subsp. verna. Experimental crossing confirmed that both parental taxa produce fertile seeds via a sexual pathway, but not by apomixis, and that both serve as pollen acceptors in heteroploid crosses, which is consistent with the plastid sequencing. However, hybridization is asymmetric, with maternal-excess crosses being significantly more successful. No signs of neoautotetraploidization or neoallotetraploidization were detected. In summary, recent gene flow between the studied Ficaria taxa is either limited or absent.

scholarly journals A central limit theorem for the parsimony length of trees

1996 ◽  
Vol 28 (04) ◽  
pp. 1051-1071 ◽  
Author(s):  
Mike Steel ◽  
Larry Goldstein ◽  
Michael S. Waterman
Keyword(s):  
Central Limit Theorem ◽  
Limit Theorem ◽  
Central Limit ◽  
Large Deviation ◽  
Null Model ◽  
Independent Random Variables ◽  
Minimum Length ◽  
Maximum Parsimony Tree ◽  
Parsimony Tree ◽  
Mean And Variance

In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed probabilities. Except in one special case, this distribution is difficult to describe exactly. Here we analyze this distribution by providing a recursive and readily computable description, establishing large deviation bounds for the parsimony length of a fixed tree on a single site and for the minimum length (maximum parsimony) tree over several sites. We also show that, under very general conditions, the former distribution converges asymptotically to the normal, thereby settling a recent conjecture. Furthermore, we show how the mean and variance of this distribution can be efficiently calculated. The proof of normality requires a number of new and recent results, as the parsimony length is not directly expressible as a sum of independent random variables, and so normality does not follow immediately from a standard central limit theorem.

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