Implications of fossil conifers for the phylogenetic relationships of living families

Fossils have played a central role in our understanding of the evolution of conifers. Interpretation of the seed cone as a compound strobilus and the homologies of the ovuliferous scales of modern conifers with the axillary dwarf shoot of Pennsylvanian forms are based on fossils. Similarly, early evolutionary trends involving the reduction, fusion, and planation of the fertile and sterile elements of the axillary dwarf shoot, leading to structures characteristic of modern families, are documented in Late Permian and Triassic conifers. However, a phylogeny elucidating the derivation of modern families from fossil forms based on shared derived features has been elusive. The present cladistic treatment using 11 characters of ovulate cones and one of pollen grains suggests three phylogenetic groups of Late Paleozoic conifers, represented loosely by the Emporicaceae, Utrechtiaceae, and Majonicaceae of Mapes and Rothwell. The Taxaceae appears to have diverged from ancestors within the Utrechtiaceae, whereas the other modern families owe their origins to the Majonicaceae. The origin of the Taxodiaceae appears to have been biphyletic.Taxodium, Cupressus andSciadopitys are strongly linked toDolmitia of the Majonicaceae, butCryptomeria, Cunninghamia andAraucaria are grouped together and diverge basal to the former taxa.Pinus branches from a position basal to the known genera of the Majonicaceae and all modern families except the Taxaceae.Podocarpus also diverges basal toMajonica but may share an ancestor with this genus;Cepahalotaxus diverges basal to theDolmitiaPseudovoltzia subclade but distal toMajonica. Similarly, the Cheirolepidiaceae originated from basal members of the Majonicaceae and shows no close phylogenetic relationship with any modern family. Except for a strong linkage betweenCycadocarpidium and theAraucariaCunninghamia subclade, genera of the Voltziaceae appear to have branched more or less independently from within the Majonicaceae and show no strong affinity with modern conifers. Thus differences between modern conifer families are due mainly to their divergence from different Paleozoic ancestors.     

ASPECTS OF CONE AND OVULE ONTOGENY IN CRYPTOMERIA (TAXODIACEAE)

The axillary complex of female cones of Cryptomeria is initiated as a tangentially extended triangular structure with a rounded apex. It is bilaterally symmetrical. Structures interpreted as prophylls are differentiated first, but they become insignificant in later development. They are succeeded by two successive pairs of lobes, each lobe being the common primordium for an adaxial ovule and a tooth. The ovule initially much exceeds the tooth. The apex of the complex has a diversity of fates and may differentiate as an ovule-tooth pair. A one-to-one relation between teeth and ovules may be lost by abortion of ovules. The initial relation between teeth and ovules is obscured in later development due to extension of tissues at the base of the complex associated with considerable enlargement of the teeth. Histogenesis of the various parts is described, together with the vascular system. There is a vascular supply to the tooth but not the ovule. The results support a direct comparison with the extinct transition conifers Pseudovoltzia and Aethophyllum but do not fully support Florin's generalized model for the arrangement of parts in the axillary complex of conifers.     

Resolving the systematic and phylogenetic position of isolated ovules: a case study on a new genus from the Permian of China

Isolated ovules occur in many fossil plant assemblages, where they provide important insights into seed‐plant diversity and evolution. However, in many cases, the ovules cannot be attributed to individual groups of seed plants, restricting systematic and evolutionary assessments that can be made from otherwise well‐characterized fossil taxa. In the present paper, we describe a new kind of ovule discovered in tuffaceous sediments from the Permian‐aged Xuanwei Formation in Guizhou Province, China. This ovule has 180° rotational symmetry and an integument comprising a variably thick sarcotesta, a uniformly thick sclerotesta and a uniformly thin endotesta. The nucellus is attached to the integument at least basally and contains a collapsed seed megaspore; a nucellar apex is absent. Both the integument and nucellus are vascularized by paired bundles in the major plane of the ovule; the integumentary bundles are considerably larger than the nucellar bundles and the nucellar bundles emerge from a conical vascular pad. Generation of a three‐dimensional reconstruction based on serial peels revealed the gross morphology and organization of the ovule and highlighted the presence of features consistent with cardiocarpalean‐type ovules (ovule shape, histological features of the integument) and also features more typical of lagenostomalean‐ and trigonocarpalean‐type ovules (large integumentary bundles, presence of nucellar bundles). To assess the affinity and evolutionary significance of the ovule, it has been included in a cladistic matrix of cardiocarpalean‐, lagenostomalean‐ and trigonocarpalean‐type ovules. Results place the ovule within the cardiocarpalean group of ovules known to have been produced by several plant groups, including cordaitean coniferophytes, pteridosperms and Palaeozoic conifers. The cladistic topology supports generic level distinction of the present species, requiring the establishment of Muricosperma guizhouensis Seyfullah & J.Hilton gen. & sp. nov . Lagenostomalean ovules produced by hydrasperman pteridosperms form a basal paraphyletic grade, whereas trigonocarpalean ovules produced by medullosan pteridosperms form a monophyletic group in which Stephanospermum is paraphyletic with respect to Rhynchosperma and Pachytesta. The results also place the Mississippian ovule Mitrospermum bulbosum apart from all of the Pennsylvanian species of Mitrospermum that form a strongly supported clade. Consequently, M. bulbosum is transferred to the new genus Whitaddera Seyfullah & J.Hilton as W. bulbosa (Long) Seyfullah & J.Hilton. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 84–108.     

Morphogenesis of the reproductive shoots of Welwitschia mirabilis and Ephedra distachya (Gnetales), and its evolutionary implications

For decades, Gnetales appeared to be closely related to angiosperms, the two groups together forming the anthophyte clade. At present, molecular studies negate such a relationship and give strong support for a systematic position of Gnetales within or near conifers. However, previous interpretations of the male sporangiophores of Gnetales as pinnate with terminal synangia conflict with a close relationship between Gnetales and conifers. Therefore, we investigated the morphogenesis of the male reproductive structures of Welwitschia mirabilis and Ephedra distachya by SEM and light microscopy. The occurrence of reduced apices to both halves of the antherophores of W. mirabilis gives strong support for the assumption that the male ‘flowers’ of W. mirabilis represent reduced compound cones. We assume that each half of the antherophore represents a lateral male cone that has lost its subtending bract. Although both halves of the antherophores of Ephedra distachya lack apical meristems, the histological pattern of the developing antherophores supports interpreting them as reduced lateral male cones as well. Therefore, the male sporangiophores of Gnetales represent simple organs with terminal synangia. Although extant conifers do not exhibit terminal synangia, similar sporangiophores are reported for some Cordaitales, the hypothetical sister group of conifers. Moreover, several Paleozoic conifers exhibit male cones with terminal sporangia or synangia. Therefore, we propose that conifers, Cordaitales and Gnetales originated from a common ancestor that displayed simple sporangiophores with a terminal cluster of sporangia.     

Highly rearranged and size‐variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

Although conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization of conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved towards reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. On the basis of cpDNA organization, our analyses revealed that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the ‘gnepines’ clade. In addition, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favours the removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data help understand the complexity and evolution of cupressophyte cpDNAs.     

TWO NEGLECTED ASPECTS OF FOSSIL CONIFERS

Most conifers, living and fossil, drop their foliage in one of two natural ways. Either each leaf is abscised separately, or intact leafy shoots are abscised. Thus, a fossil leafy shoot of a leaf-dropping species is an unusual specimen, and is the result of premature, violent removal, as by storm. Any reproductive organs it bears are likely to be immature. This idea, applied to the ovules of Taxus jurassica Florin leads to their reinterpretation: they prove unlike Taxus, but rather, like Amentotaxus. A few living conifers drop their leaves or leafy shoots at the end of each summer. There may be evidence that a fossil was deciduous. Phyllotaxis has seldom been examined closely in fossil conifers but can be clearly observed even in compressed specimens. Three main kinds occur: 1) Leaves or cone scales are attached singly in a helix (spiral) which is usually very regular. 2) Leaves are attached two (or more) at a node and those of the next node alternate strictly; if there are pairs, the next pair is at 90° decussation. 3) Leaves are in opposite pairs but the next pair is at an angle of less than 90°, and the leaves form a double helix or bijugate spiral. In fossils all three kinds can be subdivided according to the numbers of oblique rows (parastichies) rising to the right and left, in relation to the diameter of the organ. Torreya gracilis Florin (from the Jurassic) proves to have the same phyllotaxis, a double helix, as that found in modern Torreya shoots. But Florin's Taxus jurassica has its leaves in decussate pairs, unlike Taxus, but rather, like Amentotaxus. For this and other reasons it is here renamed Marskea jurassica (Florin) comb. cnov.     

Morphological divergence among Spanish Common Crossbill populations and adaptations to different pine species

Crossbills (Loxia spp.) provide a classical avian model of ecological specialization on food resources. Previous studies have suggested that morphometric, genetic and vocal diversification among Common Crossbill Loxia curvirostra populations is better explained by ecological distance (use of different conifers) than by geographical distance, indicating that populations have diverged adaptatively. We tested for adaptive divergence in Iberian crossbills using bill and body size measurements of 6082 crossbills from 27 sites, each consisting of a dominant or single pine (Pinus) of four possible species. Crossbills using different pines differed significantly in body size and bill size and shape. There was no correlation between geographical and morphological distance among sampling sites, consistent with the hypothesis that the morphological divergence of Iberian crossbills is shaped by their ecological differences (foraging on alternative conifers) rather than geographical distance. However, for unknown reasons, Common Crossbills foraging on Pinus sylvestris in Iberia have on average much smaller bills than Parrot Crossbills Loxia pytyopsittacus feeding on the same pine species in northern Europe. The extent to which crossbills specialize on Iberian P. sylvestris remains to be established. Specialization on conifers with overlapping geographical distributions may be facilitated by matching habitat choice of crossbills as a function of their local intake rates.     

The chloroplast genomes of conifers lack one of the rRNA-encoding inverted repeats

Summary Chloroplast DNA from species of five different conifer genera was extracted and studied by Southern blot analysis. For all these species, hybridization with heterologous probes specific for 16 S and 23 S rDNA detected only one chloroplast DNA fragment per enzyme digest. This observation suggests that the 16 S and 23 S rRNA genes are not duplicated in these genomes. The unique 16 S rDNA-containing BamHI fragment from Pinus contorta Dougl. was cloned and restriction mapped. Apart from the 16 S rRNA gene, this fragment also contained the psbC and psbD genes. It is concluded that the chloroplast genomes of a wide taxonomic range of conifers lack one of the inverted repeat elements and that a dislocation of the psbDC gene cluster has occurred in P. contorta.     

Isolation of embryo sacs from Dianthus ovules by enzymatic treatments and microdissection

 Mature ovules of Dianthus (Caryophyllaceae) were histologically observed by clearing and serial sectioning to characterize the cells of the embryo sac. The results show that the mature embryo sac was located deep inside the hemitropous ovule due to thick nucellar tissue at the micropylar region. For the isolation of the embryo sacs, ovules were collected from ovaries of flowers 1 day after anthesis, and treated with an enzyme solution for digesting cell walls on a gyratory shaker. After 12 h of enzyme treatment, these ovules were dissected using a glass needle under an inverted microscope to release the embryo sacs. The embryo sacs, characterized by their specific size, were successfully released by these successive treatments. The viability of the embryo sacs was more than 80% as assessed with fluorescein diacetate staining. Fluorescent staining with 4,6-diamidino-2-phenylindole revealed the nuclei of the egg apparatus in the isolated embryo sacs. The procedure for isolating embryo sacs established in this study will offer a new approach to further in vitro studies on fertilization in Dianthus. Received: 20 January 1999 / Revision received: 12 July 1999 / Accepted: 17 August 1999     

AIRFLOW PATTERNS AROUND SOME EARLY SEED PLANT OVULES AND CUPULES: IMPLICATIONS CONCERNING EFFICIENCY IN WIND POLLINATION

Aerodynamic analyses showing characteristic airflow patterns and the potential for wind-mediated pollination are presented for models of Paleozoic (Carboniferous) ovules and ovulate cupules (i.e., Genomosperma kidstoni, G. latens, Salpingostoma dasu, Physostoma elegans, Eurystoma angulare, and Stamnostoma huttonense). Lobes on ovules and cupules are shown to produce localized regions of turbulent flow with a concomitant reduction in airflow velocity. Data based upon models that mimic the characteristics of windborne pollen (= pseudopollen) show that these regions of turbulent flow correspond to those in which suspended pseudopollen impact with ovule and/or cupule surfaces. These data have bearing on a sequence of ovule morphologies purported to show the evolution of the integument by the progressive reduction in length of “preintegumentary” lobes and their acropetal fusion. As the preintegumentary lobes of the models studied consolidate around the megasporangium, regions of turbulent flow and high pseudopollen impact become localized around the pollen chamber or salpinx. The general morphologic trend envisioned for the evolution of the ovule is seen to be associated with an aerodynamic streamlining and an increased potential for wind-mediated pollination. Data for hair-bearing ovules and for ovulate cupules are discussed within the context of possible selective pressures favouring streamlining.     

Cultura in Vitro di Ovuli di Pinus Pinea L.

Abstract

Pinus Pinea ovules cultured in vitro. — The degree of growth and autonomical differentiation of Pinus pinea L. proembryo has been studied by means of controlled cultures in vitro of excised ovules.

Proembryos in vitro undergo involution and initials of their growth points change back into parenchimatoides cells.

Completely differentiated embryos cultivated in vitro behave as if they were not physiologicaly ripe in all their parts. Embryos cultured in august, september and october develop into rocotless seedlings. Only embryos cultured in november have roots able to elongate where germinating, but in a still scarce degree in comparison with hypocotile and cotiledons. Hypocotil root ratio is inverted as regards what happens in nature.

The primary endosperm of Pinus pinea L. cultivated in vitro undergoes surface diffuse proliferation.

A case of polyembriony has been observed.     

WIND POLLINATION OF TAXUS CUSPIDATA

The air disturbance patterns created by and around the ovules of Taxus cuspidata are quantified for various orientations to the direction of ambient airflow, and are shown to largely dictate the motion (vectoral trajectories) and mode of deposition of windborne pollen on ovule surfaces. Perpendicular orientation to the direction of airflow results in two regions characterized by high densities of adhering pollen — one on the windward surface of the ovule, resulting from direct inertial collision, and another on the leeward surface resulting from non-inertial sedimentation. Parallel and inclined orientations of the ovule to the direction of airflow produce quantitative and qualitative variations in the pattern of adhering pollen resulting from inertial and non-inertial deposition. Direct collision of windborne pollen grains with the micropylar ends of ovules occurs for all orientations to wind direction. The aerodynamics of the ovulate shoot complex of Taxus cuspidata is related to that previously described for conifer ovulate cones, cycad megastrobili, and simulated wind tunnel analyses of archaic Paleozoic ovules based on scale models. Water transport of pollen (adhering to integument and bract surfaces) to micropyles quantitatively alters the distribution of adhering pollen grains on ovule surfaces. Although there is no evidence that pollen grains of this species are osmotically ruptured, observations do not preclude the possibility that water transport of pollen may reduce the number of viable pollen grains reaching the micropyle.     

Foliar carbon isotope discrimination in Larix species and sympatric evergreen conifers: a global comparison

Larches (Larix spp.), deciduous conifers, occur in the northern hemisphere in cold-temperate and boreal climates – an environment normally thought to favor evergreen tree species. We compare foliar carbon isotope discrimination (Δ), instantaneous water use efficiency, total foliar nitrogen concentration, and specific leaf area (for a subset of sites) between Larix spp. and co-occurring evergreen conifers at 20 sites throughout the natural range of larches. Except for Larix occidentalis in the xeric Intermountain West, USA, Δ is significantly (P < 0.05) greater for larches than co-occurring evergreen conifers at 77% of the sites, suggesting that larches use water less efficiently. At elevations greater than 3000 m, the Δ of Larix spp. and co-occurring conifers converge, suggesting that water is not the limiting resource. Foliar nitrogen concentration and specific leaf area are two ecophysiological characteristics that are positively correlated with high photosynthetic capacity. Foliar nitrogen concentration is significantly greater for larches than evergreen conifers at 88% of the sites and specific leaf area is approximately three times greater for larches than co-occurring conifers. Future studies should examine the potential effect that global warming may have on the distribution of larch forests because the water use efficiency of larches is commonly less than co-occurring evergreen conifers and the boreal and high-latitude environments are likely to experience the greatest climate warming. Received: 23 May 1997 / Accepted: 28 October 1997     

A New Species of Petrified Ovules of Late Paleozoic

Ovules (or seeds) are distributed widely in the beds of Paleozoic of China, but what have been found are all impressions or molds of them. Recently, while studying the fossil plants in coal balls of Coal Seam No.7 (P1) at the upper part of Taiyuan Formation in Xishan Coal- Field, Taiyuan, Shanxi Province, We found a kind of petrified ovules with internal structures, which not only are abundant but also quite well presserved. Having been studied, they are put into Cardiocarpus Brongniart and considered as a new species C. samaratus. In the coal bails they are often found associated with the leaves, stems and fructifications of Cordaites, so it is very possible that these ovules belong to Cordaites. It is very interesting that these ovules are very similar to those of the earliest conifers Lebachia described by G. M. Rothwell in 1982. This indicates' that there is a close relation between Cordaites and conifers. Cardioearpus samaratus ap.nov. The ovules are small, flat and obviously-winged. The average length is 6–7mm. The largest width (nearly equal to the length) is at the lower middle part of the ovule. Wings and the top and base of the ovule bend to the same side in a varying extent. The ovule is not cordate at the base. The integument can be divided into three layers: the sarcrotesta consisting of parenchymatous cells, the sclerotesta and the endotesta consisting of longitudinally-elongated sclerenchymatous and parenchymatous cells. The lower midrile part of the nucellus is vascularized. The micropyle is elliptical in transverse section. One main vascular bundle extends upwards from the base. Before it arrives at the sclerotesta, it biforcates into two vascular bundles and extend upwards in the sarcrotesta at the wings. In the meantime, the main vascular bundle continues' to extend upwards and passes across the sclerotesta and reaches the base of the nucellus from where it extends into the nucellus.     

Rescuing Robert Brown—The Origins of Angio-Ovuly in Seed Cones of Conifers

Robert Brown (1827) recognized the distinction between the two major classes of seed plants on the basis, respectively, of exposed ovules, which receive pollen directly, and enclosed ovules, which do not, at the time of pollination. The two groups, unfortunately, became known as “Gymnosperms” and “Angiosperms”, a distinction not made by Brown. The names are, at best, useful only as identifying labels. As is established here, gymno-ovuly and angio-ovuly would have been better words and should serve as the most consistent distinguishing character among groups of seed plants. Although conifers can hardly be claimed to be members of any lineage that led to the Angiosperms, the gymno-ovulate method of reproduction must have occurred in the direct ancestors of flowering plants. Interpolating development and functional evidence serves to resurrect Robert Brown’s important but neglected observation and correct misstatements implied in generally accepted systematic terminology. The result of this approach is to discover that the conifers in their reproductive diversity show some trends indicative of those characters that define the flowering plants. Although non-homologous these character manifestations provide useful models which can lead to a better understanding of the origin of “Angiosperms” from “Gymnosperms.” In the complex and extended process of reproductive development in both major groups regular transpositions occur, depending on whether “gymno-”and “angio-”are applied to ovules or seeds. Gymno-ovuly and angio-spermy are the most common conditions in conifers but result in intrinsically opposed processes of pollen reception and subsequent seed protection, which are resolved by successive changes in seed-cone structure. The modern conifers illustrate considerable diversity of ovulate and seed cone structure in relation to several biological functions, including traits that anticipate the angio-ovulate condition, in cone inception, ovule enclosure, pollen and embryo development and seed dispersal. From the paleobotanical record we do have a good grasp of the structural changes in the progressive modification of the coniferous seed cone in conifers, starting with the antecedent Carboniferous Cordaitales. These changes have involved the progressive condensation of a lax, branched strobilus and end with the highly condensed uniovulate “cone” as in many Podocarpus species in which the equivalent of a bitegmic ovule exists. The progressive changes can be perceived typologically among existing conifers but need to be understood as the result of biological processes that suggest increased reproductive efficiency, and can be added to our present quite robust understanding of conifer phylogeny.     

The Mesozoic gymnosperms

Features needing elucidation in Mesozoic Cycadales and Bennettitales are given and the Ginkgo—Czekanowskia assemblage is surveyed. Florin's interpretation of the conifer cone scale is discussed in relation to Schweizer's work on Pseudovoltzia. Taxus jurassica Florin is revised and shown to differ generically from Taxus but to share features seen among other Taxaceae: it thus helps to unify the family, but it does not relate the Taxaceae to ordinary conifers. A possible way is offered by which early conifers like Walchia could shift their ovules from a lateral to a terminal position and if this were acceptable, then the class Taxopsida would become unnecessary.     

The origin of the ovule

Of several theories for the origin of the ovule advanced in this century and based largely on fossil evidence, the telomic concept is widely considered the most plausible. Its principal tenet is the evolution of the integument through fusion of sterile branches or telomes around a terminal megasporangium. The only point of agreement in these theories is that the entire nucellus is a megasporangium that retains a single megaspore and the endosporic female gametophyte. Their differences center on the origin of the integument. A new concept offered here on evidence from ovules of both Paleozoic and extant seed plants significantly alters the telomic theory. It proposes that the nucellus is a sporangiophore of stem origin that bears a terminal megasporangium; that at least some of the fused integumentary telomes were fertile; and that among all features cited to characterize ovules, the unique nature of the retained megaspore alone defines the seed habit. Changes in the seed plant megaspore that extended the period of nutrient absorption over the whole course of female gametophyte development, along with complex physiological changes in the nucellus, were probably achieved along a single phylogenetic line beginning in a Late Devonian population of progymnosperms. For such a combination of events to have occurred more than once is highly unlikely, and, therefore, a monophyletic origin for seed plants is proposed. Several primitive features in ovule structure, some not evidenced since the Lower Carboniferous Period, occur in a mutant form of Arabidopsis thaliana isolated from genetically transformed plants. Their recurrence provides additional support for the proposed concept of ovule origin and also suggests that the genetic mechanisms for expression of primitive features in advanced taxa could be initiated in each case by mutation of a single homeotic gene.     

Production of seedlings from ovules excised at the zygote stage in Lilium spp.

The present study was undertaken to establish a culture system for ovules excised at the zygote stage in Lilium spp. Ovules of Lilium × `Connecticut King' and L. × `Enchantment' were excised together with placental tissue 3, 5, and 10 days after pollination (DAP) and cultured on B5 medium and half-strength B5 medium containing sucrose at different concentrations. In vitro embryo development in ovules cultured at 3 DAP was influenced by the basal media and the sucrose concentration. The half-strength B5 medium with 9% sucrose was the best condition, but only a few ovules isolated from placental tissue developed into seedlings. Application of embryo culture, in which embryos were excised from ovules after 14 weeks of ovule-with-plancetal-tissue culture, greatly improved the production of seedlings. The present study indicates that a two-step culture procedure, ovule-with-placental-tissue culture and embryo culture, make it possible to produce seedlings from ovules just after fertilization.     

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein‐coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non‐conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non‐conifers. It is more obvious that in non‐conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6‐ to 3.1‐fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2‐ to 3.6‐fold of non‐conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein‐coding genes due to gene function, plant habitat, or newly acquired IRs.     

The phylogenetic position of taxaceae based on 18S rRNA sequences

The evolutionary position of the yew family, Taxaceae, has been very controversial. Some plant taxonomists strongly advocate excluding Taxaceae from the conifer order and raising its taxonomic status to a new order or even class because of its absence of seed cones, contrary to the case in the majority of conifers. However, other authors believe that the Taxaceae are not fundamentally different from the rest of the conifers except in that they possess the most reduced solitary-ovule cones. To resolve the controversy, we have sequenced the 18S rRNA genes from representative gymnosperms: Taxus mairei (Taxaceae), Podocarpus nakaii (Podocarpaceae), Pinus luchuensis (Pinaceae), and Ginkgo biloba (Ginkgoales). Our phylogenetic analysis of the new sequence data with the published 18S rRNA sequence of Zamia pumila (a cycad) as an outgroup strongly indicates that Taxus, Pinus, and Podocarpus form a monophyletic group with the exclusion of Ginkgo and that Taxus is more closely related to Pinus than to Podocarpus. Therefore, Taxaceae should be classified as a family of Coniferales. Our finding that Taxaceae, Pinaceae, and Podocarpaceae form a clade contradicts both the view that the uniovulate seed of Taxaceae is a primitive character and the view that the Taxaceae are descendants of the Podocarpaceae. Rather, the uniovulate seed of Taxaceae and that of some species of Podocarpus appear to have different origins, probably all reduced from multiovulate cones. Correspondence to: W.-H. Li