http://amborella.net/2010PlantSystematics/DATA/3-24-APG%202003%20Bot%20J%20Linn%20Soc%20APGII.pdf

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II

One of the least understood aspects of population biology is community evolution-the evolutionary interactions found among different kinds or organisms where exchange of genetic information among the kinds is assumed to be minimal or absent. Studies of community evolution have, in general, tended to be narrow in scope and to ignore the reciprocal aspects of these interactions. Indeed, one group of organisms is all too often viewed'as a kind of physical constant. In an extreme example a parasitologist might not consider the evolutionary history and responses of hosts, while a specialist in vertebrates might assume species of vertebrate parasites to be invariate entities. This viewpoint is one factor in the general lack of progress toward the understanding of organic diversification. One approach to what we would like to call coevolution is the examination of patterns of interaction between two major groups of organisms with a close and evident ecological relationship, such as plants and herbivores. The considerable amount of information available about butterflies and their food plants make them particularly suitable for these investigations. Further, recent detailed investigations have provided a relatively firm basis for statements about the phenetic relationships of the various higher groups of Papilionoidea (Ehrlich, 1958, and unpubl.). It should, however, be remembered that we are considering the butterflies as a model. They are only one of the many groups of herbivorous organisms coevolving with plants. In this paper, we shall investigate the relationship between butterflies and their food

/pdf/butterflies-and-plants-a-study-in-coevolution-59gysvp1oi.pdf

Butterflies and plants: a study in coevolution

The proposal is made that seed scientists need an internationally acceptable hierarchical system of classification for seed dormancy. Further, we suggest that a modified version of the scheme of the Russian seed physiologist Marianna G. Nikolaeva be adopted. The modified system includes three hierarchical layers – class, level and type; thus, a class may contain levels and types, and a level may contain only types. The system includes five classes of dormancy: physiological dormancy (PD), morphological dormancy (MD), morphophysiological dormancy (MPD), physical dormancy (PY) and combinational dormancy (PY + PD). The most extensive classification schemes are for PD, which contains three levels and five types (in the non-deep level), and MPD, which contains eight levels but no types. PY is not subdivided at all but probably should be, for reasons given. Justifications are presented for not including mechanical dormancy or chemical dormancy in the modified scheme. PD (non-deep level) is the most common kind of dormancy, and occurs in gymnosperms (Coniferales, Gnetales) and in all major clades of angiosperms. Since, first, this is the class and level of dormancy in seeds of wild populations of Arabidopsis thaliana and, secondly, Type 1 (to which seeds of A. thaliana belong) is also common, and geographically and phylogenetically widespread, it seems that biochemical, molecular and genetic studies on seed dormancy in this model species might have rather broad application in explaining the basic mechanism(s) of physiological dormancy in seeds.

/pdf/a-classification-system-for-seed-dormancy-33n2carxeu.pdf

A classification system for seed dormancy

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).

We examined the spatial distribution of soil nutrients in desert ecosystems of the southwestern United States to test the hypothesis that the invasion of semiarid grasslands by desert shrubs is associated with the development of "islands of fertility" under shrubs. In grasslands of the Chihuahuan Desert of New Mexico, 35-76% of the variation in soil N was found at distances <20 cm, which may be due to local accumulations of soil N under Bouteloua eriopoda, a perennial bunchgrass. The remaining variance is found over distances extending to 7 m, which is unlikely to be related to nutrient cycling by grasses. In adjacent shrublands, in which Larrea tridentata has replaced these grasses over the last century, soil N is more concentrated under shrubs and autocorrelated over distances extending 1.0-3.0 m, similar to mean shrub size and reflecting local nutrient cycling by shrubs. A similar pattern was seen in the shrublands of the Mojave Desert of California. Soil P04, Cl, SO4, and K also accumulate under desert shrubs, whereas Rb, Na, Li, Ca, Mg, and Sr are u7sually more concentrated in the intershrub spaces. Changes in the distribution of soil properties may be a useful index of desertification in arid and semiarid grasslands worldwide.

On the spatial pattern of soil nutrients in desert ecosystems

Thome, Robert F. (Rancho Santa Ana Botanic Garden, Claremont, CA 91711). Classification and geography of the flowering plants. Bot. Rev.58(3): 225–348. 1992.—This treatment of the flowering plants is the latest revision of my classification of the Class Angiospermae and replaces my 1983 and more recent 1992 synopses. An update is necessary because so much new information has been published in the last decade pertinent to the classification of the flowering plants. About 870 such recent books, monographs, and other botanical papers are cited in the Introduction, listed primarily by the botanical discipline that they represent. Also considerable changes in my classification have been necessitated by my narrowed family- and ordinal-gap concepts, acceptance of the ending “-anae” for superorders in place of the traditional but inappropriate “-iflorae,” and acceptance of more prior or more widely used names for the categories above the family. A new phyletic “shrub” replaces earlier versions, and attempts to indicate visually relative sizes and relationships among the superorders, orders, and suborders. One table includes a statistical summary of floweringplant taxa: ca. 233,900 species of 12,650 genera, 437 families, and 708 subfamilies and undivided families in 28 superorders, 71 orders, and 71 suborders of Angiospermae. Three other tables summarize the known indigenous distribution of the families and subfamilies of angiosperms about the world. The synopsis lists the flowering plant taxa from the class down to the subfamily (and in Asteraceae down to the tribe) with indication of the degree of confidence I place in the circumscription and placement of each category above the subfamily, the best available estimates of the number of genera and species for each category, and the known indigenous distribution of each subfamily and family. Table V lists alphabetically the geographical abbreviations used in the synopsis. The extensive bibliography of recent literature should be helpful to those persons interested in the classification of the flowering plants.

https://link.springer.com/content/pdf/10.1007/BF02858611.pdf

Classification and geography of the flowering plants

This update of my classification of the flowering plants, or Angiospermae, is based upon about 800 pertinent books, monographs, and other botanical papers published since my last synopsis appeared in the Nordic Journal of Science in 1983. Also I have narrowed my familyand ordinal-gap concepts to bring acceptance of family and ordinal limits more in line with those of current taxonomists. This new information and the shift in my phylogenetic philosophy have caused significant changes in my interpretation of relationships and numbers and content of taxa. Also the ending \"-anae\" has been accepted for superorders in place in the traditional but inappropriate\" -iflorae.\" A new phyletic \"shrub\" replaces earlier versions, and attempts to indicate relationships among the superorders, orders, and suborders. One table includes a statistical summary of flowering-plant taxa: ca. 235,000 species of 12,615 genera, 440 families, and 711 subfamilies and undivided families in 28 superorders, 70 orders, and 7 5 suborders of Angiospermae. Three other tables summarize the indigenous distribution of the families and subfamilies of Angiospermae about the world.

/pdf/an-updated-phylogenetic-classification-of-the-flowering-zexw27i1a6.pdf

An Updated Phylogenetic Classification of the Flowering Plants

The synopsis of my classification of the Angiospermae that was published in Aliso (Thorne, 1968) has been much modified in recent years. Increased knowledge about many of the families has resulted in a realignment of some of them and reorganization or deletion of some of the higher categories. I have published elsewhere some explanation of my classificatory modus operandi (Thorne, 1958, 1963, 1974c) and some elucidation of certain of my major groupings, such as the Araliaceae, Annoniflorae, Urti-cales, Juglandineae, Hamamelidales, Sapindineae, and Pittosporales (Thorne 1973, 1974a,b,c, 1975). I have other manuscripts near completion and have been preparing an illustrated book with full exposition of my classification of the angiosperms. Nonetheless, it seems desirable at this time to present an updated version of my synopsis of the Angiospermae with at least a brief review of my philosophy of classification, my interpretation of the probable origins of the angiosperms and their most primitive characteristics, and some elucidation of realignments that deviate considerably from other recent classifications.

A Phylogenetic Classification of the Angiospermae

/pdf/synopsis-of-a-putatively-phylogenetic-classification-of-the-1bo9htt9ki.pdf

Synopsis of a Putatively Phylogenetic Classification of the Flowering Plants

Les Myrtales selon quelques systemes de classification. Les familles et quelques caracteres: anatomie du bois, des feuilles, la fleur et son ontogenie, embryologie, la graine, caryotype et caracteristiques chimiques. Donnees sur les principales familles

Robert F. Thorne

Papers

Classification and geography of the flowering plants

An Updated Phylogenetic Classification of the Flowering Plants

A Phylogenetic Classification of the Angiospermae

Synopsis of a Putatively Phylogenetic Classification of the Flowering Plants

The order Myrtales : circumscription, variation and relationships