Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)

We analyzed sequence variation for chalcone synthase (CHS:) and alcohol dehydrogenase (ADH:) loci in 28 species in the genera ARABIDOPSIS: and ARABIS: and related taxa from tribe Arabideae. CHS: was single-copy in nearly all taxa examined, while ADH: duplications were found in several species. Phylogenies constructed from both loci confirmed that the closest relatives of Arabidopsis thaliana include Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis halleri (formerly in the genus CARDAMINOPSIS:). Slightly more distant are the North American n = 7 Arabis (BOECHERA:) species. The genus ARABIS: is polyphyletic-some unrelated species appear within this taxonomic classification, which has little phylogenetic meaning. Fossil pollen data were used to compute a synonymous substitution rate of 1.5 x 10 substitutions per site per year for both CHS: and Adh. Arabidopsis thaliana diverged from its nearest relatives about 5 MYA, and from Brassica roughly 24 MYA. Independent molecular and fossil data from several sources all provide similar estimates of evolutionary timescale in the Brassicaceae.     

Intra- and interspecific DNA variation and codon bias of the alcohol dehydrogenase (Adh) locus in Arabis and Arabidopsis species

Sequence variation at the alcohol dehydrogenase (Adh) locus was analyzed for six species each of the genera Arabis and Arabidopsis. Phylogenetic analysis showed that investigated species were grouped into three clusters, and the generic classification did not correspond to the clusterings. The results indicated that the genera could not be distinguished on the basis of the Adh variation. A significant difference in the ratio of silent to replacement sites was detected by MK test in two comparisons, with Arabidopsis thaliana polymorphism due to excess silent divergence. Silent changes were predominant in the evolution of the Adh locus in Arabis and Arabidopsis. To infer evolutionary significance of silent substitutions, codon bias was studied. The degree of codon bias of the Adh region was relatively constant over Arabis and Arabidopsis species. "Preferred" codons of A. thaliana were determined. No evidence of natural selection on codon change was detected in the Adh regions of A. thaliana and Arabis gemmifera.     

Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S-25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis, Cardaminopsis, Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.     

Phylogenetic signatures of adaptation: The Arabis hirsuta species aggregate (Brassicaceae) revisited

The mustard family, Brassicaceae, is well-known for its homoplasy in almost any morphological character at practically all taxonomic levels. The genus Arabis, within the largest tribe of the Brassicaceae, is such an example comprising numerous para- and polyphyletic groups of taxa. Past research during the last 15 years has unraveled many phylogenetic relationships among the ∼550 (or more) species within the notoriously difficult tribe Arabideae. The European Arabis hirsuta species aggregate has remained unexplored, however. Herein we analyze phylogenetic relationships using nuclear ITS and plastid DNA sequences of Eurasian Arabis to characterize Hairy rock cress (A. hirsuta) and its relatives. Representative geographic sampling is used to study character and trait evolution, and bioclimatic data are used to differentiate between species. Our overview puts European Arabis into a reliable evolutionary framework, and we provide some striking insights into evolutionary trends and correlating morphological characters from seeds and flowers with environmental data such as climate variables and elevation. We demonstrate independent parallel evolution of sets of traits, and, therefore, we could further elaborate our previous findings that within tribe Arabideae high speciation rates are correlated with perennial growth form and occurrence at higher elevation. Finally some taxonomical remarks are provided to give added context.     

Molecular Phylogenetic Studies of Brassica,Rorippa,Arabidopsis and Allied Genera Based on the Internal Transcribed Spacer Region of 18S–25S rDNA

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S–25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis,Cardaminopsis,Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.     

CHROMOSOME NUMBERS IN COMPOSITAE VIII: HELIANTHEAE

One hundred and ninety-three new counts are reported for the tribe Heliantheae of Compositae, mostly based on determinations of meiotic material, including first counts for the genera Adenothamnus, Chrysogonum, Enceliopsis, Guardiola, Isocarpha, Lipochaeta, Otopappus, and Oyedaea, as well as first counts for 66 species. The original counts are discussed in relation to those previously reported for the tribe, by genera and subtribe. Two-thirds of the approximately 150 genera and more than a third of the roughly 1500 species have now been examined. The incomplete knowledge of generic relationships in the tribe often make the interpretation of these chromosome numbers difficult. Three observations are documented and discussed: (1) genera with low chromosome numbers are few; (2) genera with aneuploid series are abundant; and (3) the original basic chromosome number in the tribe is probably in the range of x = 8 to x = 12.     

Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis

The angiosperm family Brassicaceae contains both the research model Arabidopsis (Arabidopsis thaliana) and the agricultural genus Brassica. Comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, the reduced genome size and chromosome number (n = 5) of Arabidopsis complicates comparisons. Arabidopsis shows extensive genome and chromosome reshuffling compared to its close relatives Arabidopsis lyrata and Capsella rubella, both with n = 8. To facilitate comparative genomics across the Brassicaceae we recently outlined a system of 24 conserved chromosomal blocks based on their positions in an ancestral karyotype of n = 8, rather than by their position in Arabidopsis. In this report we use this system as a tool to understand genome structure and evolution in Boechera stricta (n = 7). B. stricta is a diploid, sexual, and highly self-fertilizing species occurring in mostly montane regions of western North America. We have created an F(2) genetic map of B. stricta based on 192 individuals scored at 196 microsatellite and candidate gene loci. Single-nucleotide polymorphism genotyping of 94 of the loci was done simultaneously using an Illumina bead array. The total map length is 725.8 cM, with an average marker spacing of 3.9 cM. There are no gaps greater than 19.3 cM. The chromosomal reduction from n = 8 to n = 7 and other genomic changes in B. stricta likely involved a pericentric inversion, a chromosomal fusion, and two reciprocal translocations that are easily visualized using the genomic blocks. Our genetic map will facilitate the analysis of ecologically relevant quantitative variation in Boechera. Sequence data from this article can be found in the GenBank/EMBL data libraries under accession numbers DU 667459 to DU 708532.     

Chromosome arrangement and nuclear architecture but not centromeric sequences are conserved between Arabidopsis thaliana and Arabidopsis lyrata

In contrast to the situation described for mammals and Drosophila, chromosome territory (CT) arrangement and somatic homologous pairing in interphase nuclei of Arabidopsis thaliana (n = 5) are predominantly random except for a more frequent association of the chromosomes bearing a homologous nucleolus organizer region. To find out whether this chromosome arrangement is also characteristic for other species of the genus Arabidopsis, we investigated Arabidopsis lyrata ssp. lyrata (n = 8), one of the closest relatives of A. thaliana. First, we determined the size of each chromosome and chromosome arm, the sequence type of centromeric repeats and their distribution between individual centromeres and the position of the 5S/45S rDNA arrays in A. lyrata. Then we demonstrated that CT arrangement, homologous pairing and sister chromatid alignment of distinct euchromatic and/or heterochromatic regions within A. lyrata interphase nuclei are similar to that in A. thaliana nuclei. Thus, the arrangement of interphase chromosomes appears to be conserved between both taxa that diverged about 5 million years ago. Since the chromosomes of A. lyrata resemble those of the presumed ancestral karyotype, a similar arrangement of interphase chromosomes is also to be expected for other closely related diploid species of the Brassicaceae family.     

Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana

We examined microsatellite variation in two diploid, outcrossing relatives of Arabidopsis thaliana, Arabis petraea and Arabis lyrata. The primer sequences were derived from A. thaliana. About 50% (14 loci) of the A. thaliana primers could successfully amplify microsatellites in the related species. Analysis of microsatellite structure in the related species showed that there had been large changes in the microsatellites: there were large differences in repeat numbers and many of the A. thaliana simple repeats were shorter in the related species. For the loci we compared, the related species had a much lower level of variability at the microsatellites than Japanese wild populations of A. thaliana. This is presumably related to the different microsatellite structures, because allozyme data showed that the outcrossing relatives were highly polymorphic compared to other outcrossing herbaceous species. Use of microsatellites in assessing variability or phylogenetic relationships between different species requires caution, because changes in microsatellite structure may alter evolutionary rates.      

CHROMOSOME NUMBERS IN COMPOSITAE V. ASTEREAE II.

Reports of 100 new chromosome counts are made for the tribe Astereae of Compositae, mostly based on determinations of meiotic material, including first counts for 9 genera and 53 species. Counts are now available for 58 of the approximately 100–120 genera and 431 of the approximately 2000 species in the tribe. Comparisons are made between chromosome number and habit and also between chromosome number and geographical distribution. Species and genera with a basic number of x = 9 are the most abundant. Within different phyletic lines x = 9 is also the most abundant number. On the other hand, many species with x = 4 and 5, belonging to a number of small, largely annual genera, are concentrated in southwestern North America. The low chromosome number in these plants is probably correlated with the dry habitat they occupy, and is most likely a specialized condition.     

The genus Artemisia (Asteraceae: Anthemideae) at a continental crossroads: molecular insights into migrations, disjunctions, and reticulations among Old and New World species from a Beringian perspective

Artemisia is the largest genus (ca. 350-500+ spp.) in the tribe Anthemideae and is composed of ecologically, morphologically, and chemically diverse species that are found primarily throughout the Northern Hemisphere. Two major centers of diversity for the genus are located in Eurasia and western North America, but phytogeographic links connecting these two regions are observed all across the North Pacific Rim and adjacent areas in the Arctic, including many islands and archipelagos. Previous phylogenetic studies have helped to clarify major lineages and identify likely sister relationships, but many questions remain unanswered regarding the relationships and migration history of New and Old World species. Here we investigate the phylogenetics of Artemisia within a biogeographic context centered in the Beringian Region and offer new hypotheses concerning species relationships, migration history, and the likely role of reticulate evolution in the genus. Our sampling included many new taxa and emphasized multiple accessions of widespread species, species from proposed refugia, and species with disjunct/vicariant distributions. The ITS phylogeny contained 173 accessions (94 new and 79 from GenBank) and indicated that Artemisia is paraphyletic by the exclusion of several small Asian genera and the North American genus Sphaeromeria. Following a survey of thirteen chloroplast loci, phylogenies based on two plastid markers (psbA-trnH and rpl32-trnL spacers) were constructed with a reduced data set, and though largely consistent with the ITS topology, revealed several cases of possible introgression among New World and Beringian species. Our analysis reveals that North American Artemisia species have multiple origins, and that western North America has served as a source for some colonizing elements in eastern Asia and South America.     

The evolution of Batesian mimicry within the North American Asidini (Coleoptera: Tenebrionidae)

The asidine darkling beetles (Coleoptera: Tenebrionidae: Asidini) are a diverse tribe of flightless tenebrionids found in many arid and sub‐arid habitats around the world. The 263 currently described North American species are contained in ten genera, all of which are restricted to the western half of the continent. The Asidini, like all members of the subfamily Pimeliinae, lack defensive glands. Instead, several phenotypic traits occur within the tribe that may help limit predation. These include the contrasting defensive strategies of crypsis, through either background matching or pattern disruption, and Batesian mimicry of the chemically defended genus Eleodes. Dorsal elytral morphology was assessed between 53 North American asidine species and 13 common Eleodes model species using multiple methodologies to assess similarities between species in the two groups that might indicate mimetic relationships. A phylogeny of the North American asidines is used to map the occurrence of differing defensive strategies within the tribe. Crypsis is reconstructed as the ancestral state, with two origins for Batesian mimicry and multiple reversals. The combination of strongly to weakly cryptic species and varying levels of mimetic fidelity to Eleodes model species make the asidines a promising lineage upon which to further explore the evolution of defensive phenotypes.     

Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rDNA, and LEAFY

A phylogeny of the tribe Neillieae (Rosaceae), which comprises Neillia, Stephanandra, and Physocarpus, was reconstructed based on nucleotide sequences of several regions of cpDNA, the ITS and ETS regions of rDNA, and the second intron of LEAFY, to elucidate relationships among genera and species in Neillieae and to assess the historical biogeography of the tribe. Phylogenetic analyses indicated that Physocarpus and Neillia-Stephanandra were strongly supported as monophyletic and suggested that Stephanandra may have originated by hybridization between two lineages of Neillia. Dispersal-vicariance analyses suggested that the most recent common ancestor of Neillieae may have occupied eastern Asia and western North America and that Physocarpus and Neillia-Stephanandra may have been split by an intercontinental vicariance event in the early Miocene. The biogeographic analyses also suggested that species of Neillia and Stephanandra diversified in eastern Asia, whereas in Physocarpus one dispersal event from western North America to eastern Asia occurred. Two divergent types of LEAFY sequences were found in the eastern North American species, P. opulifolius, but only one type was present in each plant. The two types of sequences may represent homeologous genes that originated by hybridization between P. capitatus and P. monogynus, both western North American species.     

Evolution of genome size in Brassicaceae

BACKGROUND AND AIMS: Brassicaceae, with nearly 340 genera and more than 3350 species, anchors the low range of angiosperm genome sizes. The relatively narrow range of DNA content (0.16 pg < 1C < 1.95 pg) was maintained in spite of extensive chromosomal change. The aim of this study was to erect a cytological and molecular phylogenetic framework for a selected subset of the Brassicacae, and use this as a template to examine genome size evolution in Brassicaceae. METHODS: DNA contents were determined by flow cytometry and chromosomes were counted for 34 species of the family Brassicaceae and for ten Arabidopsis thaliana ecotypes. The amplified and sequenced ITS region for 23 taxa (plus six other taxa with known ITS sequences) were aligned and used to infer evolutionary relationship by parsimony analysis. KEY RESULTS: DNA content in the species studied ranged over 8-fold (1C = 0.16-1.31 pg), and 4.4-fold (1C = 0.16-0.71 pg) excluding allotetraploid Brassica species. The 1C DNA contents of ten Arabidopsis thaliana ecotypes showed little variation, ranging from 0.16 pg to 0.17 pg. CONCLUSIONS: The tree roots at an ancestral genome size of approximately 1x = 0.2 pg. Arabidopsis thaliana (1C = 0.16 pg; approximately 157 Mbp) has the smallest genome size in Brassicaceae studied here and apparently represents an evolutionary decrease in genome size. Two other branches that represent probable evolutionary decreases in genome size terminate in Lepidium virginicum and Brassica rapa. Branches in the phylogenetic tree that represent probable evolutionary increases in genome size terminate in Arabidopsis halleri, A. lyrata, Arabis hirsuta, Capsella rubella, Caulanthus heterophyllus, Crucihimalaya, Lepidium sativum, Sisymbrium and Thlaspi arvense. Branches within one clade containing Brassica were identified that represent two ancient ploidy events (2x to 4x and 4x to 6x) that were predicted from published comparative mapping studies.     

天门冬科黄精族细胞学研究进展

在全面收集和整理黄精族染色体数据的基础上,对国内外有关黄精族各类群间的染色体数目和倍性的变化规律进行了总结,并从染色体的多倍化和非整倍化与系统发育关系和地理分布方面探讨了黄精族内各属的起源和演化关系问题。黄精族包括黄精属、舞鹤草属、异黄精属和竹根七属,共约100余种,其中舞鹤草属(x=18)、异黄精属(x=16)和竹根七属(x=20)的染色体基数稳定,而黄精属染色体基数波动较大,主要为x=8~16,既有多倍化也有非整倍化现象。染色体数据表明黄精族4个属的染色体进化模式各不相同,揭示了黄精族内染色体从高基数向低基数演化的规律;各属内染色体的演化主要是体现在二倍体水平上的核型变异,多倍化在本族中不占主导地位;仅黄精属内伴有非常强烈的非整倍化现象;细胞学证据与分子系统发育的结果比较吻合,为黄精族内属间以及属下的系统发育与进化提供了重要的参考资料。     

Systematics and karyoevolution inMagnoliidae:Tetrameranthus as compared with otherAnnonaceae genera of the same chromosome number

First generic chromosome counts reveal the base number x=7 for the generaTetrameranthus andRollinia. T. umbellatus from the Peruvian Amazon is diploid (2n=14),T. duckei from Brazil (Manaus) is tetraploid (2n=28). In the NeotropicsRollinia (7 species counted) has developed diploid to octoploid taxa (2n=14, 28, 42, 56). Counts of 7 South AmericanAnnona species are presented for comparison (2n=14, 28). The West AfricanCleistopholis patens has 2n=14. The Asian genusMezettia: 2n=14 and the neotropicalGuatteria tribe: 2n=28 are also revised. A detailed karyomorphological comparison, including karyotypes, banding patterns, condensing behaviour of chromosomes and structure of interphase nuclei reveals that the closely related generaAnnona andRollinia are almost identical in their diploid genomes, whereas the polyploid ones differ in their heterochromatin (=hc) composition and number of NO-chromosomes.Cleistopholis, Mezettia and theGuatteria tribe are karyologically and systematically distinct from each other and fromAnnona/Rollinia. Tetrameranthus as compared with the karyomorphology of about 60 other Annonaceous genera has a very peculiar and unusual karyomorphology which underlines its isolated position. Nuclear structures are almost identical in the African genusUvariopsis (2n = 16) and partly similar in theGuatteria tribe; both also share some morphological similarities and possibly are related. From a comparison ofTetrameranthus with several nuclear types within theMagnoliidae, a new model of chromosome evolution in primitive Angiosperms is suggested. In respect to their eco-morphological differentiation the genera investigated differ strongly from each other.Dedicated to Prof. Dr. K.-H.Rechinger on the occasion of His 80th birthday.     

First chromosome number determinations in south-eastern South American species of Lupinus L. (Leguminosae)

Chromosome numbers are presented for the first time for 30 accessions of nine south-eastern South American Lupinus species. Chromosome numbers of 2 n = 32 and 34 were found for L. bracteolaris (three out of five accessions with 2 n = 32) and L. linearis (two out of three accessions with 2 n = 32), and of 2 n = 36 for L. gibertianus , L. lanatus, L. magnistipulatus , L. multiflorus , L. rubriflorus , L. reitzii and L. uleanus . All the South American species examined have relatively low chromosome numbers when compared with most of the Old World and North American species. Our results, where 2 n = 36 is the rule, are in sharp contrast to the data for North American Lupinus species and reveal the following: (1) low chromosome numbers are the rule, at least in the southern part of eastern South America; (2) cytologically, the eastern South American species form a group distinct from the North American taxa; (3) high levels of polyploidy have not played as important a role in evolution and speciation in eastern South America as in North America; (4) the predominance of low chromosome numbers in eastern South American species and the existence of similar numbers in two of the six rough-seeded Old World species support the hypothesis that in the evolution of the genus the eastern South American species branched off first, followed by the rough-seeded group.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Socety , 2002, 139 , 395–400.     

Molecular phylogeny and biogeography of tribe anthemideae (Asteraceae), based on chloroplast gene ndhF

Anthemideae (Asteraceae) is primarily a north temperate, Old World tribe of 109 genera and approximately 1740 species. We sequenced a 1200-bp portion of chloroplast gene ndhF for representative genera and subtribes and constructed a phylogeny for the tribe. There is support for monophyly of subtribes Chrysantheminae and Gonosperminae and for portions of some subtribes. However, our molecular phylogeny differs significantly from traditional classifications and from previously published morphological phylogenies of the tribe. Many South African genera from several different subtribes form a basal grade, indicating multiple, relictual lineages. Eurasian genera form a recently derived clade that includes the Mediterranean genera of the Iberian Peninsula and North Africa. There is little resolution or support for the placement of eastern Asian genera. Apparently, the tribe originated in the Southern Hemisphere, presumably in Africa, with the Eurasian and Mediterranean members being derived from a common ancestor.     

CHROMOSOME NUMBERS IN COMPOSITAE. IX. HAPLOPAPPUS AND OTHER ASTEREAE

Reports of 209 original chromosome counts are made for the tribe Astereae of Compositae, including first counts for two genera and 46 species or subspecies. With over 80 % of the species counted, chromosome numbers are now available for all North American sections of Haplopappus. Two major groupings are apparent: one, with basic numbers of x = 4, 5, or 6, is basically herbaceous; the other, with x = 9, consists of shrubs or subshrubs. Aneuploidy is known only in the “herbaceous” group of Haplopappus, and polyploidy is more extensive there than in the woodier group of sections.