Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous

Ribosomal ITS sequences and plant phylogenetic inference.

The {ITS} region of nuclear ribosomal {DNA}: {A} valuable source of evidence on angiosperm phylogeny

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

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Genome evolution in polyploids

The coding region of the mat K gene and two intergenic spacers, psb A-trn H and trn L(UAA)-trn F(GAA), of cpDNA were sequenced to study phylogenetic relationships of 32 Paeonia species. In the psb A-trn H intergenic spacer, short sequences bordered by long inverted repeats have undergone inversions that are often homoplasious mutations. Insertions/deletions found in the two intergenic spacers, mostly resulting from slipped-strand mispairing, provided relatively reliable phylogenetic information. The mat K coding region, evolving more rapidly than the trnL-trn F spacer and more slowly than the psb A-trn H spacer, produced the best resolved phylogenetic tree. The mat K phylogeny was compared with the phylogeny obtained from sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA. A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent. The Eurasian and western North American disjunct distribution of the genus may have resulted from interrruption of the continuous distribution of ancestral populations of extant peony species across the Bering land bridge during the Miocene. Pleistocene glaciation may have played an important role in triggering extensive reticulate evolution within section Paeonia and shifting distributional ranges of both parental and hybrid species.

Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).

The internal transcribed spacers and the 5.8S coding region of nuclear ribosomal DNA were sequenced and analyzed to address questions of generic relationships in Winteraceae. The molecular data generated a single tree that is congruent with one based on morphological data. The sequences of ITS 1 in the family range from 235 to 252 bases in size and of ITS 2 from 213 to 226 bases. The size of the 5.8S coding region is 164 bases. The range of ITS 1 and ITS 2 sequence divergence between pairs of genera within Winteraceae is relatively low in comparison to other plant families. Two types of ITS 1 and ITS 2 sequences were observed in the same individual for some taxa. Sequence variations between the two arrays are 4.70/-o 6.3% for ITS 1 and 5. 10/o-7.0% for ITS 2. Both arrays of sequences, however, generate the same phylogenetic relationships. Rates of nucleotide substitutions for the internal transcribed spacers are 3.2-5.2 x 10-'? substitution per site per year estimated in ITS 1 and 3.6-5.7 x 10-'? in ITS 2.

Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of Ribosomal DNA in Winteraceae

The ndhF sequences of 99 taxa, representing all sections in extant Magnoliaceae, were analyzed to address phylogenetic questions in the family. Magnolia macrophylla and M. dealbata, North American species of Magnolia section Rytidospermum, are placed at the base in the subfamily Magnolioideae although its supporting value is low. In the remaining taxa, several distinctive lineages are recognized: (1) Magnolia, the biggest genus in the family, is not monophyletic; (2) Michelia, including section Maingola of Magnolia subgenus Magnolia, is closely related with Elmerrillia and sections Alcimandra and Aromadendron of Magnolia subgenus Magnolia; (3) the associates of Michelia are grouped with Magnolia subgenus Yulania and section Gynopodium of Magnolia subgenus Magnolia; (4) Pachylarnax forms a clade with sections Manglietiastrum and Gynopodium of Magnolia; (5) a well-supported Manglietia clade is recognized; (6) Caribbean species of section Theorhodon of Magnolia subgenus Magnolia, which are section Splendentes sensu Vazquez-Garcia, are closely allied with New World members of Magnolia subgenus Talauma; and (7) section Rytidospermum of Magnolia subgenus Magnolia and subgenus Talauma are polyphyletic. The separated clades in the molecular tree are considerably different from traditional taxonomic dispositions in the family. The molecular data strongly suggest that a taxonomic realignment of infrafamilial delimitations and compositions should be considered.

Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences.

http://amborella.net/2011-Graduate-PS/Week9-Multigene%20analyses%20HGT/Kim%20et%20al%202004a%20MPE%20Ranunculales.pdf

Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody?

Phylogenetic analyses of ten chloroplast DNA regions, ndhF, rbcL, matK, ORF350, trnL intron, trnL-trnF, trnH-psbA, rbcL-atpB, trnK 5′ intron, and trnK 3′ intron (8,719 bp in aligned sequences) from 48 selected taxa were carried out to address phylogenetic questions in the family Magnoliaceae. The major clades in the molecular tree are considerably different from the currently suggested classification system and from the traditionally recognized subgroups in the family. Eleven major clades were recognized with strong support in the subfamily Magnolioideae: (1) MICHELIA clade: Michelia, Elmerrillia, sect. Maingola, sect. Alcimandra, and sect. Aromadendron, (2) YULANIA clade: subgen. Yulania, (3) GYNOPODIUM clade: Pachylarnax, sect. Manglietiastrum, and sect. Gynopodium, (4) KMERIA clade: Kmeria, (5) THEORHODON clade: sect. Theorhodon sensu stricto (excluding sect. Splendentes, which was recently separated from sect. Theorhodon) and sect. Magnolia, (6) GWILLIMIA clade: sect. Gwillimia, sect. Lirianthe, and sect. Blumiana, (7) TALAUMA clade: sect. Talauma and sect. Splendentes, (8) MANGLIETIA clade: Manglietia, (9) RYTIDOSPERMUM clade: sect. Rytidospermum sensu stricto (excluding Magnolia fraseri, M. macrophylla, and M. dealbata) and sect. Oyama, (10) FRASERI clade: M. fraseri, and (11) MACROPHYLLA clade: M. macrophylla and M. dealbata. The recognition of eleven major clades in the subfamily Magnolioideae in this study is in good agreement with previous molecular studies based on less sampling or fewer DNA regions. All of these eleven clades were highly supported with bootstrap values exceeding 80% in both maximum parsimony and maximum likelihood analyses and with posterior probabilities exceeding 0.98 in a Bayesian analysis. However, detailed relationships among the major clades were weakly supported. The molecular data suggest that the taxonomic circumscription of infrafamilial delimitations and compositions should be reconsidered.

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Phylogeny of Magnoliaceae based on ten chloroplast DNA regions

We report a partial ndhF sequence (1528 bp) of Magnolia latahensis and a partial rbcL sequence (699 bp) of Persea pseudocarolinensis from the Clarkia fossil beds of Idaho, USA (Miocene; 17-20 million years [my] BP). The ndhF sequence from M. latahensis was identical to those of extant M. grandiflora, M. schiediana, M. guatemalensis, and M. tamaulipana. Parsimony analysis of the ndhF sequence of M. latahensis and previously reported ndhF sequences for Magnoliaceae placed M. latahensis within Magnolia as a member of the Theorhodon clade. This result is reasonable considering that: (1) the morphology of M. latahensis is very similar to that of extant M. grandiflora, and (2) a recent molecular phylogenetic study of Magnoliaceae showed that the maximum sequence divergence of ndhF among extant species is very low (1.05% in subfamily Magnolioideae) compared with other angiosperm families. We reanalyzed the previously reported rbcL sequence of M. latahensis with sequences for all major lineages of extant Magnoliales and Laurales. This sequence is sister to Liriodendron, rather than grouped with a close relative of M. grandiflora as predicted by morphology and the results of the ndhF analysis, possibly due to a few erroneous base calls in the sequences. The rbcL sequence of P. pseudocarolinensis differed from rbcL of extant Persea species by 3-6 nucleotides and from rbcL of extant Sassafras albidum by two nucleotides. Phylogenetic analyses of rbcL sequences for all major lineages of Magnoliales and Laurales placed the fossil P. pseudocarolinensis within Lauraceae and as sister to S. albidum. These results reinforce the suggestion that Clarkia and other similar sites hold untapped potential for molecular analysis of fossils.

DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae)

Youngbae Suh

Papers

Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of Ribosomal DNA in Winteraceae

Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences.

Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody?

Phylogeny of Magnoliaceae based on ten chloroplast DNA regions

DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae)