Fossils and seed plant phylogeny reanalyzed

In a cladistic analysis of Recent seed plants, Loconte and Stevenson (1990) obtained results that conflict with our 1986 analysis of both extant and fossil groups and argued that fossil data had led us to incorrect conclusions. To explore this result and the general influence of fossils on phylogeny reconstruction, we assembled new “Recent” and “Complete” (extant plus fossil) data sets incorporating new data, advances in treatment of characters, and those changes of Loconte and Stevenson that we consider valid. Our Recent analysis yields only one most parsimonious tree, that of Loconte and Stevenson, in which conifers are linked with Gnetales and angiosperms (anthophytes), rather than with Ginkgo, as in our earlier Recent and Complete analyses. However, the shortest trees derived from our Complete analysis show five arrangements of extant groups, including that of Loconte and Stevenson and our previous arrangements, suggesting that the result obtained from extant taxa alone may be misleading. This increased ambiguity occurs because features that appear to unite extant conifers and anthophytes are seen as convergences when fossil taxa are interpolated between them. All trees found in the Complete analysis lead to inferences on character evolution that conflict with those that would be drawn from Recent taxa alone (e.g., origin of anthophytes from plants with a “seed fern” morphology). These results imply that conclusions on many aspects of seed plant phylogeny are premature; new evidence, which is most likely to come from the fossil record, is needed to resolve the uncertainties.     

Fossils and ferns in the resolution of land plant phylogeny

Fifty-two taxa of living and extinct vascular plants were evaluated in an unconstrained numerical cladistic analysis using 101 morphological characters to simultaneously resolve the phylogenetic relationships of ferns sensu lato. Included in the analysis were ferns assignable to the Cladoxylales, Stauropteridales, Rhacophytales, Zygopteridales, Ophioglossales, Marattiales, Filicales, and Hydropteridales, as well as a rhyniophyte, a trimerophyte, equisetophytes, lignophytes, and the psilotophytesPsilotum andTmesipteris. The results placed ferns and fernlike plants in three distinct clades, indicating that ferns s.l. are a polyphyletic grade group. Fern clades consist of extinct stauropterids; extinct cladoxylaleans, rhacophytaleans, and zygopteridaleans; and eusporangiates and leptosporangiates with living and extinct species. Psilotophytes occur near the base of the tree rather than nesting with the Filicales, as hypothesized by some. These results place Ophioglossales as the sister group to Marattiales plus the leptosporangiates, supporting the hypothesis that Ophioglossales represent ferns rather than progymnosperms. These analyses are a first attempt, which includes extinct plants, to develop cladistic hypotheses for the overall topology of fern phylogeny and to lay the groundwork for more detailed analyses of relationships among the homosporous leptosporangiates.     

Fossils and phylogeny uncover the evolutionary history of a unique antipredator behaviour

Recently, two squirrel species (Spermophilus spp.) were discovered to anoint their bodies with rattlesnake scent as a means of concealing their odour from these chemosensory predators. In this study, we tested multiple species with predator scents (rattlesnake and weasel) to determine the prevalence of scent application across the squirrel phylogeny. We reconstructed the evolutionary history of the behaviour using a phylogenetic analysis and fossil records of historic predator co‐occurrence. Squirrels with historical and current rattlesnake co‐occurrence all applied rattlesnake scent, whereas no relationship existed between weasel scent application and either weasel or rattlesnake co‐occurrence. This was surprising because experimental tests confirmed rattlesnake and weasel scent were both effective at masking prey odour from hunting rattlesnakes (the primary predator of squirrels). Ancestral reconstructions and fossil data suggest predator scent application in squirrels is ancient in origin, arising before co‐occurrences with rattlesnakes or weasels in response to some other, now extinct, chemosensory predator.     

Taxon sampling and seed plant phylogeny

We investigated the effects of taxon sampling on phylogenetic inference by exchanging terminals in two sizes of rbcL matrices for seed plants, applying parsimony and bayesian analyses to ten 38‐taxon matrices and ten 80‐taxon matrices. In comparing tree topologies we concentrated on the position of the Gnetales, an important group whose placement has long been disputed. With either method, trees obtained from different taxon samples could be mutually contradictory and even disagree on groups that seemed strongly supported. Adding terminals improved the consistency of results for unweighted parsimony, but not for parsimony with third positions excluded and not for bayesian analysis, particularly when the general time‐reversible model was employed. This suggests that attempting to resolve deep relationships using only a few taxa can lead to spurious conclusions, groupings unlikely to be repeatable with different taxon samplings or larger data sets. The effect of taxon sampling has not generally been recognized, and phylogenetic studies of seed plants have often been based on few taxa. Such insufficient sampling may help explain the variety of phylogenetic hypotheses for seed plants proposed in recent years. We recommend that restricted data sets such as single‐gene subsets of multigene studies should be reanalyzed with alternative selections of terminals to assess topological consistency.     

Linnaeus' sexual system and flowering plant phylogeny

Carl Linnaeus brought order to the knowledge of plants and animals by arranging all known species in encyclopaedic works. He proposed a system of plants, the sexual system, based on the number and arrangement of male and female organs. His artificial sexual system has since long been replaced by 'natural' or phylogenetic systems but there has never been a comprehensive comparison of the sexual system with modern plant classification. The currently most often used classification of flowering plants is the APG-system. It is based on comprehensive phylogenies of flowering plants, reconstructed by analyses of DNA data. The APG-system covers all flowering plants which are classified in 453 families and these are classified in 45 orders. Most of the species were not known at time of Linnaeus. Families and orders in the APG-system are arranged in larger informal groups representing major branches in the flowering plant phylogenetic tree. Three such groups are the monocots, the rosids, and the asterids.
I have examined all genera published in Species plantarum (1753) and classified them according to order and major groups in the APG-system. All classes except one, number 15 Tetradynamia, comprises groups of unrelated plants. Not surprisingly, the sexual system does not display what we know today about plant relationships. As is evident from this analysis, there is little correspondence between the sexual system and the APG-system. This does not mean that the sexual system has been useless or misleading. When it was introduced, it formed the basis for much intensified research and increased knowledge of plants.     

Sexual selection,sexual dimorphism and plant phylogeny

Summary Darwin examined sexual dimorphism in animals, arguing that sexual selection was important in the evolution of such dimorphism. Sexual dimorphism in plants may have parallel causes and costs.The processes that contribute to sexual dimorphism may also lead to speciation and morphological differences among related species, as argued originally by Darwin. Where sexes are separate and dimorphism is well-developed, males of related animal species (both vertebrate and invertebrate) are often strikingly different from each other, while females may be virtually indistinguishable. A similar pattern may exist in plants: it is frequently the males (of dioecious taxa) or the male portions of the flower (in co-sexual flowers) that apparently have diversified. I suggest that the similarity of pattern may be accounted for by a similarity of process.In addition, sexual selection may have contributed to certain evolutionary trends within the angiosperms and, indeed, to angiosperm radiation.     

ESTimating plant phylogeny: lessons from partitioning

Background  

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains difficult. Sequencing errors and orthology determination are the major problems when using ESTs as a source of characters for systematics. Here we develop methods to incorporate EST sequence information in a simultaneous analysis framework to address controversial phylogenetic questions regarding the relationships among the major groups of seed plants. We use an automated, phylogenetically derived approach to orthology determination called OrthologID generate a phylogeny based on 43 process partitions, many of which are derived from ESTs, and examine several measures of support to assess the utility of EST data for phylogenies.     

Higher plant origins and the phylogeny of green algae

Summary 5S rRNA sequences from six additional green algae lend strong molecular support for the major outlines of higher plant and green algae phylogeny that have been proposed under varying naming conventions by several authors. In particular, the molecular evidence now available unequivocally supports the existence of at least two well-separated divisions of the Chlorobionta: the Chlorophyta and the Streptophyta (i.e., charophytes) (according to the nomenclature of Bremer). The chlamydomonad 5S rRNAs are, however, sufficiently distinct from both clusters that it may ultimately prove preferable to establish a third taxon for them. In support of these conclusions 5S rRNA sequence data now exist for members of four diverse classes of chlorophytes. These sequences all exhibit considerably more phylogenetic affinity to one another than any of them show toward members of the other cluster, the Streptophyta, or the twoChlamydomonas strains. Among the Charophyceae, new 5S rRNA sequences are provided herein for three genera,Spirogyra, Klebsormidium, andColeochate. All of these sequences and the previously publishedNitella sequence show greater resemblance among themselves and to the higher plants than they do to any of the other green algae examined to date. These results demonstrate that an appropriately named taxon that includes these green algae and the higher plants is strongly justified. The 5S rRNA data lack the resolution needed, however, to unequivocally determine which of several subdivisions of the charophytes is the sister group of the land plants. The evolutionary diversity ofChlamydomonas relative to the other green algae was recognized in earlier 5S rRNA studies but was unanticipated by ultrastructural work. These new data provide further evidence for the relative uniqueness of the chlamydomonads and are discussed further.     

Fossils and lithostratigraphy

It is proposed that any future revision of the International Stratigraphic Guide should explicitly approve the use of characteristic faunal and floral assemblages in the definition of lithostratigraphical units, providing that the fossils are readily observable and identifiable in the field and assist in the mapping of the rocks.     

Fossils and Strata

Jessen, H. L.: Schultergürtel und Pectoralflosse hci Actinopterygiern. [Shoulder girdle and pectoral fin in actinopterygians.] Fossils and Strata , Number 1, pp. 1–101, Pls. 1–25. Oslo, 5th May 1972.
The anatomy of the shoulder girdle and pectoral fin is investigated in adults and larvae of Asperser, Amia, Lepisosteus, Elops, Salmo , and Polypterus . In comparison with similar structures in other gnathostomian fishes these studies yielded certain conclusions as concerns the interrelationships of the recent actinopterygian groups and the affinities of the hrachiopterygians, the latter by this evidence belonging to an evolutionary line of their own. With regard to actinopterygian phylogeny, a comparison with the shoulder girdle and pectoral fin in fossil forms, including Chondrosteus, Moythomoasia, Palaeoniscus, Pteronisculus, Pachycormus, Catarus, Hypsocormus , and Birzeria , shows that teleosteans presumably are closer to chondrosteans than holosteans, and that holosteans seem to have branched off comparatively early from the actinopterygian stem.     

丛枝菌根真菌群落与植物系统发育的相关性分析

为弄清丛枝菌根(arbuscular mycorrhiza, AM)真菌群落随宿主植物演化的变异规律,通过对MaarjAM数据库进行数据挖掘, 根据每个分子虚拟种(virtual taxa, VT)包含的DNA序列不少于5条的标准, 筛选出188种菌根植物。通过分析植物与其根内AM真菌的关系发现: AM真菌的物种丰富度随着寄主植物的分化而增加; 在不同的植物系统类群中, AM真菌的物种丰富度显著不同; 在起源时间较晚的被子植物和裸子植物中, AM真菌的物种丰富度显著高于起源较早的苔类、角苔类和蕨类植物类群, 而与寄生植物共生的AM真菌物种丰富度与早期植物无显著差异; 不同寄主植物进化类群间AM真菌组成差异显著。以上结果表明: AM真菌群落随着寄主植物进化而发生变化。在进化过程中, 寄主植物倾向于选择保留共生效率较高的AM真菌。     

Correlation analysis between arbuscular mycorrhizal fungal community and host plant phylogeny

 为弄清丛枝菌根(arbuscular mycorrhiza, AM)真菌群落随宿主植物演化的变异规律,通过对MaarjAM数据库进行数据挖掘, 根据每个分子虚拟种(virtual taxa, VT)包含的DNA序列不少于5条的标准, 筛选出188种菌根植物。通过分析植物与其根内AM真菌的关系发现: AM真菌的物种丰富度随着寄主植物的分化而增加; 在不同的植物系统类群中, AM真菌的物种丰富度显著不同; 在起源时间较晚的被子植物和裸子植物中, AM真菌的物种丰富度显著高于起源较早的苔类、角苔类和蕨类植物类群, 而与寄生植物共生的AM真菌物种丰富度与早期植物无显著差异; 不同寄主植物进化类群间AM真菌组成差异显著。以上结果表明: AM真菌群落随着寄主植物进化而发生变化。在进化过程中, 寄主植物倾向于选择保留共生效率较高的AM真菌。