Hydrophobia of gymnosperms: myth or reality? A global analysis

According to the classical textbooks, the gymnosperms are the only seed plants without aquatic species. Recently, however, a set of virtually complete compilations on gymnosperms has been published, enabling a new evaluation of the putative hydrophobia of gymnosperms. This synthesis aims at portraying the relation of all extant gymnosperm species to aquatic and wetland habitats. We present a database of all 986 extant gymnosperm species with their ecological characteristics including 291 cycads, 80 gnetophytes, one ginkgophyte and 614 conifers. We define four categories reflecting the level of hydrophobia and hydrophily of all species and their possible adaptation to wetlands and/or aquatic habitats. Eighty‐two percent (805) of the extant species of gymnosperms are clearly hydrophobic, but 18% (180) are classified as hydrophilic. The podocarp Retrophyllum minus is the only obligate inhabitant of aquatic habitats. This contribution classifies gymnosperms into four categories in reference to their physiological and morphological adaptation to a moisture gradient. It relativizes the putative hydrophobia of gymnosperms and provides new perspectives for research on gymnosperms.

Related papers:

title: Physiological and molecular basis of susceptibility and tolerance of rice plants to complete submergence.
abstract: Rice plants are much damaged by several days of total submergence. The effect can be a serious problem for rice farmers in the rainfed lowlands of Asia, and runs contrary to a widespread belief amongst plant biologists that rice is highly tolerant of submergence. This article assesses the characteristics of the underwater environment that may damage rice plants, examines various physiological mechanisms of injury, and reviews recent progress achieved using linkage mapping to locate quantitative traits loci (QTL) for tolerance inherited from a submergence-tolerant cultivar FR13A. Progress towards identifying the gene(s) involved through physical mapping of a dominant tolerance locus on chromosome 9 is also summarized. Available physiological evidence points away from responses to oxygen shortage as being inextricably involved in submergence injury. An imbalance between production and consumption of assimilates is seen as being especially harmful, and is exacerbated by strongly accelerated leaf extension and leaf senescence that are ethylene-mediated and largely absent from FR13A and related cultivars. DNA markers for a major QTL for tolerance are shown to be potentially useful in breeding programmes designed to improve submergence tolerance.

title: A Handbook of the World's Conifers
abstract: Foreword Preface The conifers of the world, an introduction The distribution and ecology of conifers The economic importance of conifers The conservation of conifer diversity Synopsis of families and genera Taxonomic treatment of families, with keys to families Taxonomic treatment of genera and species (in alphabetical order), with keys to sections, subsections and species Glossary References Lists of illustrations Index to botanical names of conifers

title: The botany of mangroves
abstract: Preface Acknowledgements Part I. General Account: 1. Ecology 2. Floristics 3. Biogeography 4. Shoot systems 5. Root systems 6. Water relations and salt balance 7. Flowering 8. Seedlings and seeds 9. Utilization and exploitation Part II. Detailed Descriptions by Family References Index.

title: The Biology of Mangroves and Seagrasses
abstract: 1. Mangroves and seagrasses 2. Mangroves and their environment 3. Seagrasses and their environment 4. Community structure and dynamics 5. The mangrove community: terrestrial components 6. The mangrove community: marine components 7. Seagrass communities 8. Measuring and modelling 9. Comparisons and connections 10. Biodiversity and biogeography 11. Impacts 12. Global climate change

title: A comparitive study of the hydrophyte flora from the Alpine Rhine to the Middle Rhine. Application to the conservation of the Upper Rhine aquatic ecosystems
abstract: A typology of the main channel of the river Rhine according to its aquatic bryophyte and vascular hydrophyte assemblages is presented. The aquatic bryophytes are especially abundant in the main channel, having found stable, rocky habitats with variable water levels in the regulated river, and segregate longitudinally along a gradient of water quality. Conversely, the vascular hydrophytes are restricted to side channels with constant discharges and silt deposits, and segregate laterally along a gradient of connectivity with the main river. The hydrophytes have been affected by water eutrophication which became obvious in the 1960s–1970s. The oligotrophic groundwater-fed side-channels disconnected since the river canalization consequently include a relic reference flora. Important hydraulic works are currently in progress in order to protect the areas located downstream from the canalized Rhine from flooding by retaining the river waters in lateral systems during the discharge peaks and to recreate a functional alluvial floodplain by reconnecting the disconnected side-channels to the main river. The floodpulse caused by the suddent input of surface water in the disconnected brooks will probably wash out most of the hydrophytes and it is very likely that the rare species with their low recolonization strategies will disappear in these conditions. It is highly desirable to preserve from flooding the last oligotrophic brooks with their original hydrophyte assemblages. Those brooks which show a tendency to silt up can be re-dynamized by ecological engineering without disturbing the flowing drains of the watertable. In areas (including flowing drains of the watertable) that have already been designated for flood retention, the hydraulic works should allow, as far as possible, the preservation of the flowing oligotrophic streams by only permitting the input of surface water in the silted-up brooks. The disconnected side-channels could then continue their role as refugia from where the main channel, whose water quality has been improving for a decade, could be recolonized by its primary flora.

title: Fungal biodiversity in aquatic habitats
abstract: Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.

title: Cycads of the world
abstract: This is a comprehensive reference to the cycads of the world. Part One details their biology and cultivation, and pests and diseases to which they are susceptible. The second section provides concise descriptions of each plant, with information on its habitat and distribution, and horticultural information on seed germination, growing conditions and propagation methods where known. Species entries are accompanied by colour photographs and illustrations. This reference is designed to be of interest to scientists and to general readers interested in the conservation and cultivation of cyclads in public and private gardens.

title: Conifers of the World: The Complete Reference
abstract: Researched for more than three decades, this definitive work provides up-to-date descriptions of all the true conifers of the world, including 545 species of trees and shrubs. Written for accessibility to both horticultural and botanical audiences, it is the first comprehensive update of conifer taxonomy in nearly a century. Noted conifer taxonomist James E. Eckenwalder also discusses the relationships among the groups, practical usages, champion trees, fossil occurrences, and biology. New identification guides for the families and genera are based whenever possible on foliage features and thus should be easier to use than traditional conifer keys, which focus on seasonal, and often microscopic, cone characters. Eckenwalder shares the reasoning behind his taxonomic decisions, many of which are unique to this book, reflecting a comprehensive reevaluation of conifer classification. He also outlines the features sought in cultivars of each genus, particular cultivation concerns, and conifers recommended for cultivation under various conditions and to achieve different effects. Some 3,000 cultivars have been available in recent times, more than five times the total number of conifer species. Several hundred original illustrations include drawings of the seed cones for all genera as well as for representative species. Maps of the natural distribution of each genus allow for easy comparison of ranges. Handsome black-and-white photographs of species in their natural habitats and attractive color photos further enrich the volume. More than 100 images reproduce foliage of many genera as an aid in identification. With its unprecedented attention to detail and extensive bibliography, this major work is an essential reference for botanists, naturalists, and horticulturists.

title: Conifers Around the World: Conifers of the Temperate Zones and Adjacent Regions
abstract: Being a trailblazer at heart, I normally have little use for the plethora of hiking books on the market. But when Michael sent me of copy of Conifer Country, I couldn’t resist reading it. I was a little disappointed that the rest of the biota was left out, because botanical endemism is particularly high in the Klamath Range. Of course, the author had to focus his efforts and, with 39 conifers recorded in the region (even without the Del Norte pine, which is still in question), he had more to work with than in any other temperate mountain range of its size on the planet. The first part of the book covers climate, geology and the tree species. Well over half of the book is dedicated to Klamath conifers and their distribution and his maps are the best yet. I found some mis-statements in the section describing the conifers. For example, in the section for gray pine (Pinus sabiniana) (pages 84-86), the 500 to 2,500 ft. elevation range should be from nearly sea level to 7,000 feet elevation (at Sawtooth Peak, Inyo County), and that the pine is dependent on fire to regenerate is misleading because both birds and rodents are involved. The description of its distribution in Oregon as outlier populations that naturalized from plantings for food or landscaping in recent human history was refuted in a 2009 article in this journal (Kalmiopsis 16:1-14). On page 99, the author states that an underlying band of serpentine that runs east to west from the mountains to the coast north of the Chetco is an edaphic barrier to northward movement of redwoods. These serpentine belts actually run north to south; rather than inhibited by this substrate, coast redwood thrives on weathered serpentine-derived soils. Then on page 113, he comments that “Alaska-cedar trees do not reach significant size in the Siskiyous–I’ve never seen one more than 35’ tall.” I’ve seen Alaska cedars 70 feet tall and nearly 3 feet in diameter on Whiskey Peak in the Oregon Siskiyous. These and a few other errors will be corrected in the second edition, coming soon. The remainder of the book is all about hikes, but not to worry, none of these is anywhere as long as the Pacific Crest Trail or the Desert Trail, which both extend from the Mexican border and to the Canadian border. If you are a teacher, with a three month vacation, you might have enough time to complete the PCT in one season, or you can complete a half dozen of the 29 hikes listed in Conifer Country. The author is a teacher and clearly he has put his time to good use by writing this intriguing book (that is not only for teachers). The important thing to remember is to select hikes that are within your capability and time frame and be prepared to deal with the elements and strenuous climbs. Be sure to take time to smell the conifers and explore the geology and hydrology. When you are fit enough, you may want to do the Iron Man hike a.k.a. the 400-mile Bigfoot Trail mentioned at the end of the book. If you push so long and hard that you think you’ve just seen Bigfoot, it’s time to take a break! Is he really out there? Well, you will just have to take the trail and discover for yourself. This book is well written and very readable, the color photography is superb and just enough black and white photos to draw you into the mountains to see the real colors. Would I recommend that you buy the book, well no, not unless you get off your duff and put it to good use! This guide to the Klamath Mountains can give you an experience of a lifetime. Don’t pass up the opportunity, and be sure to take the book with you (carry it in a zip-lock bag to keep the elements out). –Frank Callahan, Siskiyou Chapter.

title: Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.
abstract: Efforts to resolve Darwin's "abominable mystery"-the origin of angiosperms-have led to the conclusion that Gnetales and various fossil groups are sister to angiosperms, forming the "anthophytes." Morphological homologies, however, are difficult to interpret, and molecular data have not provided clear resolution of relationships among major groups of seed plants. We introduce two sequence data sets from slowly evolving mitochondrial genes, cox1 and atpA, which unambiguously reject the anthophyte hypothesis, favoring instead a close relationship between Gnetales and conifers. Parsimony- and likelihood-based analyses of plastid rbcL and nuclear 18S rDNA alone and with cox1 and atpA also strongly support a gnetophyte-conifer grouping. Surprisingly, three of four genes (all but nuclear rDNA) and combined three-genome analyses also suggest or strongly support Gnetales as derived conifers, sister to Pinaceae. Analyses with outgroups screened to avoid long branches consistently identify all gymnosperms as a monophyletic sister group to angiosperms. Combined three- and four-gene rooted analyses resolve the branching order for the remaining major groups-cycads separate from other gymnosperms first, followed by Ginkgo and then (Gnetales + Pinaceae) sister to a monophyletic group with all other conifer families. The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms, such as "flower-like" reproductive structures and double fertilization, were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales. An initial angiosperm-gymnosperm split implies a long stem lineage preceding the explosive Mesozoic radiation of flowering plants and suggests that angiosperm origins and homologies should be sought among extinct seed plant groups.

title: Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
abstract: Phylogenetic relationships among the five groups of extant seed plants are presently quite unclear. For example, morphological studies consistently identify the Gnetales as the extant sister group to angiosperms (the so-called "anthophyte" hypothesis), whereas a number of molecular studies recover gymnosperm monophyly, and few agree with the morphology-based placement of Gnetales. To better resolve these and other unsettled issues, we have generated a new molecular data set of mitochondrial small subunit rRNA sequences, and have analyzed these data together with comparable data sets for the nuclear small subunit rRNA gene and the chloroplast rbcL gene. All nuclear analyses strongly ally Gnetales with a monophyletic conifers, whereas all mitochondrial analyses and those chloroplast analyses that take into account saturation of third-codon position transitions actually place Gnetales within conifers, as the sister group to the Pinaceae. Combined analyses of all three genes strongly support this latter relationship, which to our knowledge has never been suggested before. The combined analyses also strongly support monophyly of extant gymnosperms, with cycads identified as the basal-most group of gymnosperms, Ginkgo as the next basal, and all conifers except for Pinaceae as sister to the Gnetales + Pinaceae clade. According to these findings, the Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and Gnetales (e.g., double fertilization and flower-like reproductive structures) arose independently.

title: Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms.
abstract: The popular view that plant mitochondrial genome evolves slowly in sequence has been recently challenged by the extraordinarily high substitution rates of mtDNA documented mainly from several angiosperm genera, but high substitution rate acceleration accompanied with great length variation has been very rarely reported in plant mitochondrial genes. Here, we studied evolution of the mitochondrial rps3 gene that encodes the ribosomal small subunit protein 3 and found a dramatically high variation in both length and sequence of an exon region of it in Conifer II. A sequence comparison between cDNA and genomic DNA showed that there are no RNA editing sites in the Conifer II rps3 gene. Southern blotting analyses of the total DNA and mtDNA, together with the real-time PCR analysis, showed that rps3 exists as a single mitochondrial locus in gymnosperms. It is very likely that the Conifer II rps3 gene has experienced retroprocessing, i.e., the re-integration of its cDNA into the mitochondrial genome, followed by an evolutionary acceleration due to the intron loss. In addition, the phylogenetic analysis of rps3 supports the sister relationship between conifers and Gnetales. In particular, the monophyly of conifer II is strongly supported by the shared loss of two rps3 introns. Our results also indicate that the mitochondrial gene tree would be affected in topology when the "edited" paralogs are analyzed together with their genomic sequences.

title: A natural history of conifers
abstract: Conifers are the most diverse, interesting, beautiful trees in the world, so why is it that our gardens are home to so few species? Part of the reason lies in their economic importance which, by focusing attention on relatively few species, has limited our understanding of one of the most remarkable plant groups on earth. Leading expert Aljos Farjon provides a broader perspective with this compelling narrative that observes conifers from the standpoint of the curious naturalist. It starts with the basic question of what conifers are and continues to explore their evolution, taxonomy, ecology, distribution, human uses, and issues of conservation. As the story unfolds many popular misconceptions are dispelled, such as the notion that all conifers have cones (untrue), and the extraordinary diversity of conifers begins to dawn as Farjon describes the diminutive creeping shrub Microcachrys tetragona, whose strange seed cones resemble raspberries, and the prehistoric-looking Araucaria meulleri. The taxonomic diversity of conifers is huge and Farjon goes on to relate how, over the course of 300 million years, these trees and shrubs have adapted to survive geological upheavals, climatic extremes, and formidable competition from flowering plants. Scarcely less remarkable is his explanation of how conifers, with only 627 species, grew to occupy every continent on earth ranging from the high latitudes to the tropics. This illuminating review will fascinate plant lovers who wish to discover the extraordinary relatives of ordinary garden conifers, natural historians, who will relish seeing conifers reviewed in a broad context, and all who seek to learn more about the early history of life on our planet.

title: Out of China: distribution history of Ginkgo biloba L.
abstract: Gingko biloba L. is one of the most mysterious plant species, which continues to attract the interest of scientists and the public since many centuries. However, our knowledge of its evolutionary history and worldwide distribution is limited. Herein we are combining evidence from a previous phylogeographic analysis of Ginkgo biloba's range in China using cpDNA and AFLPs with new data from old, early introduced in Korea, Japan, Europe and Northern America with the aim to unravel the early human-mediated introduction history of this species. We provide evidence that Ginkgo biloba reached Japan via different routes from China during the last two millennia most likely by human-mediated dispersal. Based on AFLP data, all individuals originally introduced to Europe and North America (e.g., by Kaempfer in Europe in the 1720s) are genetically similar to one ofthe Korean accessions raising, the question ofthe validity of the origin of Kaempfer's original material, which was said to be brought from Japan to Europe in the early 18th century. Multiple introduction into Korea and Japan in concert with an out-crossing mating system has maintained high levels of gene diversity; this is also true for the European and North American trees. In addition, the trees outside the original Chinese Pleistocene refugia, due to their relatively small gene-pool, have a reduced number of AFLP fragments and no exclusive alleles.

title: The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates
abstract: BackgroundWelwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.ResultsThe chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR). Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony) or as the sister to Pinus (the only conifer representative) in a monophyletic gymnosperm clade (maximum likelihood, bayesian). Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants.ConclusionAlthough the basic organization of the Welwitschia plastome is typical, its compactness, gene content and high nucleotide divergence rates are atypical. The current lack of additional conifer plastome sequences precludes any discrimination between the gnetifer and gnepine hypotheses of seed plant relationships. However, both phylogenetic analyses and shared genome features identified here are consistent with either of the hypotheses that link gnetophytes with conifers, but are inconsistent with the anthophyte hypothesis.

title: The origin and diversification of angiosperms.
abstract: The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of eudicots include Ranunculales, which are sister to all other eudicots, and a clade of core eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and eudicots, (2) branching order among basal eudicots, (3) relationships among the major clades of core eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.

title: Cypress knees: an enduring enigma.
abstract: less, throughout the nineteenth century and continuing to the present, botanists have put forth hypotheses about the function of these peculiar formations, hypotheses that have mcluded aeration of the root system, vegetative reproduction, mechanical support, nutrient accumulation, and carbohydrate storage. The aeration theory has been the most popular and, indeed, is presented without question in some botany texts, but in fact, no explanation has been generally accepted.’ 1

title: Why Are There So Many Kinds of Flowering Plants
abstract: The world is amazingly rich in the numbers of living species of plants and animals; understanding this diversity and explaining its origin continues to be a central issue in evolutionary biology. Whether working in the dry, but speciesrich, Sonoran Desert or in the epiphyteladen cloud forests in Central America, one is confronted by the same general question: What factors have caused such diverse communities to evolve? In a stimulating paper on animal diversity, Hutchinson (1959) pointed out that the species richness of the contemporary biota on land far exceeds species numbers in the oceans. He suggested that flowering plants have played a major role in the evolution of terrestrial diversity. There is no compelling evidence for the existence of angiosperms before the Cretaceous, but recently scientists have acquired a much more detailed understanding of their differentiation in the Middle Cretaceous (Dilcher 1979, Doyle 1977, Doyle and Hickey 1976). Since then, the flowering plants have come to dominate a great majority of the world's terrestrial ecosystems.

title: Why Are There So Many Species of Flowering Plants
abstract: This essay is in part a reply to the companion one by Burger and in part supplementary to it. Since the topic is to a large extent one of taxonomy or systematicsand reflects also the evolutionary history of a class of organisms over 120 million years-data from systematics are essential, and paleontological data must be considered when they are available.

title: The tortoise and the hare: ecology of angiosperm dominance and gymnosperm persistence
abstract: Gymnosperms, and conifers in particular, are sometimes very productive trees yet angiosperms dominate most temperate and tropical vegetation. Current explanations for angiosperm success emphasize the advantages of insect pollination and seed dispersal by animals for the colonization of isolated habitats. Differences between gymnosperm and angiosperm reproductive and vegetative growth rates have been largely ignored. Gymnosperms are all woody, perennial and usually have long reproductive cycles. Their leaves are not as fully vascularized as those of angiosperms and are more stereotyped in shape and size. Gymnosperm tracheids are generally more resistant to solute flow than angiosperm vessels. A consequence of the less efficient transport system is that maximum growth rates of gymnosperms are lower than maximum growth rates of angiosperms in well lit, well watered habitats. Gymnosperm seedlings may be particularly uncompetitive since their growth depends on a single cohort of relatively inefficient leaves. Later, some gymnosperms attain a higher productivity than co-occurring angiosperm trees by accumulating several cohorts of leaves with a higher total leaf area. 
 
 
 
These functional constraints on gymnosperm growth rates suggest that gymnosperms will be restricted to areas where growth of angiosperm competitors is reduced, for example, by cold or nutrient shortages. Biogeographic evidence supports this prediction since conifers are largely confined to high latitudes and elevations or nutrient-poor soils. Experimental studies show that competition in the regeneration niche (between conifer seedlings and angiosperm herbs and shrubs) is common and significantly affects conifer growth and survival, Fast-growing angiosperms, especially herbs and shrubs, may also change the frequency of disturbance regimes thereby excluding slower-growing gymnosperms. 
 
 
 
Shade-tolerant and early successional conifers share similar characteristics of slow initial growth and low plasticity to a change in resources. Shade-tolerant gymnosperms would be expected to occur only where forest openings are small or otherwise unsuitable for rapid filling by fast-growing angiosperm trees, lianas or shrubs. The limited evidence available suggests that shade-tolerant conifers are confined to forests with small gap sizes where large disturbances are very rare. 
 
 
 
The regeneration hypothesis for gymnosperm exclusion by angiosperms is consistent with several aspects of the fossil record such as the early disappearance of gymnosperms from early successional environments where competition with angiosperms would have been most severe. However there are unresolved difficulties in interpreting process from paleoecological pattern which prevent the testing of alternative hypotheses.

title: Conifer Reproductive Biology
abstract: Prologue.- Glossary.- Section I. Conifer Reproductive Biology Overview. 1. Introducing Conifers.- 2. The Diplohaplontic Life Cycle.- Section II.  The Male Gametophyte Enclosed in a Pollen Wall.- 6.  Pollination and Fertilization.- 7. Syngamy, Embryo Development and Seed Dispersal.-Section III.  Form and Chance. 8. The Dynamic Wind-Pollinated Mating System.- 9. The Embryo Lethal System.-

title: Threatened plants of New Caledonia: Is the system of protected areas adequate?
abstract: With 76% of its 3063 native species of flora endemic, the New Caledonia biodiversity hotspot has long been recognized as having a high potential for conservation. Under the new IUCN Red List categories, 25% of the endemic plants are at risk (Conservation Dependent, Vulnerable, Endangered, Critically Endangered), and five species are already extinct. A review of their distribution demonstrates that 83% of the threatened species do not occur at all in a conservation area, and only 11% have their conservation status improved by a protected area. The protected area network is geographically and floristically very unbalanced, with the rainforest and high altitude maquis in the south concentrating most of the conservation effort. Conversely, the middle and northern segments of the island, as well as all of the dry west coast, are left without adequate conservation area. Two vegetation types, the sclerophyll forest and the unique low/middle altitude maquis, are virtually totally unprotected. We conclude that the current network of protected areas needs to be considerably expanded, in terms of both geographical/floristic subregions within New Caledonia and vegetation type covered. With only 54% of the conservation area covered by strict mining restrictions, existing reserves need to have their conservation efficiency improved by a more vigorous enforcement of their status, and by extending mining bans to all of them.

title: Size and function in conifer tracheids and angiosperm vessels.
abstract: The wide size range of conifer tracheids and angiosperm vessels has important consequences for function. In both conduit types, bigger is better for conducting efficiency. The gain in efficiency with size is maximized by the control of conduit shape, which balances end-wall and lumen resistances. Although vessels are an order of magnitude longer than tracheids of the same diameter, they are not necessarily more efficient because they lack the low end-wall resistance of tracheids with torus-margo pits. Instead, vessels gain conducting efficiency over tracheids by achieving wider maximum diameters. End-walls contributed 56-64% to total xylem resistance in both conduit types, indicating that length limits conducting efficiency. Tracheid dimensions may be more limited by unicellularity and the need to supply strength to homoxylous wood than by the need to protect against cavitation. In contrast, the greater size of the multicellular vessel is facilitated by fibers that strengthen heteroxylous wood. Vessel dimensions may be most limited by the need to restrict intervessel pitting and cavitation by air-seeding. Stressful habitats that promote narrow vessels should favor coexistence of conifers and angiosperms. The evolution of vessels in angiosperm wood may have required early angiosperms to survive a phase of mechanic and hydraulic instability.

title: An overview of plant responses to soil waterlogging
abstract: Under natural conditions, plants are frequently exposed to transient or permanent soil waterlogging. Flooding drastically influences the soil physico-chemical properties, most notably soil redox potential, pH and O2 level. Thus, conditions of hypoxia or anoxia are commonly encountered by plant root systems. These O2 restrictive conditions dramatically affect plant growth, development and survival. One of the best characterised plant responses to soil waterlogging is the metabolic switch from aerobic respiration to anaerobic fermentation. In fact, most proteins induced during hypoxic conditions are enzymes involved in the establishment of this fermentative pathway. Because the plant cells need to keep a continuous ATP supply, the use of alternative electron acceptors and/or alternative pathways may be key elements of survival under soil waterlogging. The plant response may also include a reduction in stomatal conductance and photosynthesis, as well as root hydraulic conductivity. These physiological modifications may in turn affect carbohydrate reserves and translocation. In fact, efficient use of carbohydrates may discriminate between tolerant and intolerant species. Other observed adaptations include morphological changes which comprise the formation of hypertrophied lenticels, the initiation of adventitious roots and/or the development of aerenchyma. Our knowledge of the basic adaptive mechanisms of plants to soil waterlogging has benefited from large scale genomic and proteomic approaches, however, the diversity of the adaptive responses involved underlines the difficulty when studying this stress. This update reviews our current comprehension of the metabolic, physiological and morphological responses and adaptations of plants to soil waterlogging.

title: Waterlogging stress in plants: A review
abstract: Waterlogging is the major obstacle for sustainable agriculture. Plants subjected to waterlogging suffer from substantial yield losses. Under natural environmental conditions, plants often get exposed to transient or permanent waterlogging. Flooding induces a number of alterations in important soil physiochemical properties like soil pH, redox potential and oxygen level. Thus, the plants growing on the waterlogged soil face the stressful environment in terms of hypoxia (deficiency of O2) or anoxia (absence of O2). These oxygen deficient conditions substantially hamper plant growth, development and survival. Plants under O2-restrictive environment exhibit metabolic switch from aerobic respiration to anaerobic fermentation. It is evident from the available literature that most of the genes expressed under flooding stress are potentially involved in the synthesis of enzymes known to play active role in the establishment of this fermentative pathway. Plants undergo this metabolic change in order to get continuous supply of Adenosine triphosphate (ATP). Under waterlogged conditions, plants exhibit several responses including hampered stomata conductance, net CO2-assimilation rate and root hydraulic conductivity. Furthermore, plants grown under waterlogged conditions often face the oxidative damage induced by the generation of reactive oxygen species. These reactive oxygen species in turn affects the integrity of membranes and induce damage to the efficiency of photosystem II, thereby, causing considerable decrease in net photosynthetic rates. Moreover, these perturbations in physiological mechanisms may affect the carbohydrate reserves and translocations. In fact, waterlogging tolerant and sensitive plant species could be discriminated on the basis of their efficient carbohydrate utilization. Waterlogging is also known to induce adverse effects on several physiological and biochemical processes of plants by creating deficiency of essential nutrients like nitrogen, magnesium, potassium, calcium. Apart from these waterlogging-induced alterations in physiological mechanisms, plants growing under flooded conditions also exhibit certain morphological changes entailing the formation of adventitious roots, initiation of hypertrophied lenticels and/or establishment of aerenchyma. Therefore, the aim of this review is to highlight the major morphological, physiological and biochemical adaptations of plants to tolerate the flooding stress. 
 
  Hypoxia, anoxia, fermentation, Adenosine triphosphate (ATP), reactive oxygen species (ROS), antioxidants.

title: Effect of flooding on growth, stem anatomy, and ethylene production of Pinushalepensis seedlings
abstract: Flooding of soil for 43 days greatly altered growth and stem anatomy and increased ethylene production by stems of 10-month-old Pinushalepensis seedlings. Flooding reduced the dry weight increment of seedlings primarily as a result of decay of roots and, to a lesser extent, inhibition of growth of roots and needles. Flooding did not influence height growth of seedlings but increased stem diameter, largely because of an increase in bark thickness at all stem heights and stem hypertrophy associated with proliferation of phloem parenchyma cells and an increased amount of intercellular space in the phloem. The effects of flooding on xylem increment varied appreciably with stem height. In the submerged portion of the stem, flooding greatly reduced the number of tracheids laid down per radial file. Flooding also slightly reduced the number of tracheids produced in the portion of the stem just above the water level. In the upper stem, however, flooding had little effect on xylem increment and on tracheid product...

title: Evolution of Water Transport and Xylem Structure
abstract: Land plants need water to replace the evaporation that occurs while atmospheric CO2 is diffusing into photosynthetic tissue. The water‐for‐carbon exchange rate is poor, and evolutionary history indicates a progression of innovations for cheap water transport—beginning in order with capillary suction at cell walls, stomatal regulation, hydroids, tracheids, secondary xylem, endodermis, and vessels. The radiation of plants in the Silurian and Devonian occurred when the need for water was at an all‐time low because of high CO2 concentration. Transport improvements appeared as water demand increased and CO2 dropped to current values in the Carboniferous and Permian. Stomatal regulation and high‐conductivity conduits permitted larger plants and a transition from poikilohydric to homoiohydric water relations. The evolution of conduits from hydroids through tracheids to vessels reflects the need to balance resistance to implosion and cavitation versus maximum hydraulic conductance and minimum conduit investment. Localization of rigidifying lignin away from the lumen surface and porous wall regions during tracheid evolution, and the origin of pits, acted to maintain wall strength and permeability while minimizing cavitation. Vessels mark the pinnacle of efficiency, making vines and dense, stiff woods possible without sacrificing conductivity or cavitation resistance. However, vessels make cavitation‐resistant wood more expensive and may compromise refilling efficiency versus tracheids. Vascular networks maximize hydraulic conductivity and protection from cavitation at minimum investment by following Murray’s law and localizing resistances to the periphery. A future challenge is to quantify the significance of xylem structure in terms of the carbon cost of transpiration and the net carbon profit via gas exchange.

title: THE CONCEPT OF A HYDROPHYTE FOR WETLAND IDENTIFICATION
abstract: deepwater aquatic systems and terrestrial systems. Although often found along rivers, lakes, ponds, and estuaries, wetlands also exist on gentle slopes or in isolated depressions surrounded by uplands. Wetlands can be considered to occur along a natural soil-moisture gradient between permanently flooded deepwater areas and dryland . Wetland hydrologic conditions, therefore, range from permanent inundation by shallow water or permanent soil saturation to periodic inundation or soil saturation.

title: Morphology, anatomy, and upland ecology of large cordaitalean trees from the Middle Pennsylvanian of Newfoundland
abstract: We describe the morphology and anatomy of large cordaitalean trees, preserved in Pennsylvanian (Bolsovian) alluvial deposits in southwest Newfoundland. Remains include more than one hundred calcite-permineralized stumps, trunks, and branches, including the largest cordaitalean trunk ever discovered, as well as common adpressed leaves. Reproductive organs are not preserved. We propose a sterile reconstruction of this tree based on directly attached organs and anatomical similarities between isolated, but facies-associated, organs. At ≤ 48.5 m high, mature cordaitaleans were the tallest trees in the Pennsylvanian tropical zone, and consisted of a straight, unbranched trunk topped by a dark, shading canopy, similar in gross morphology to extant araucarian conifers. A comprehensive review of the taphonomic occurrences of these large cordaitalean remains suggests that they grew in alluvial fan and extrabasinal terrains across Euramerica, and represent the earliest widespread upland forests.

title: Cordaiteans in paleotropical wetlands: An ecological re-evaluation
abstract: Cordaiteans in cordaite-dominated permineralized peat from Pennsylvanian coals in Iowa have been reconstructed as mangroves using root anatomy, peat taphonomy, and geochemical data. Macrofloral, palynofloral, and conodont biostratigraphy indicate that these peats come from the latest Atokan Blackoak coal and earliest Desmoinesian Cliffland coal (mid-Moscovian), both in the Kalo Formation. Thus, their depositional setting can be used to evaluate the mangrove hypothesis. In Recent mires, thick mangrove peats have accumulated in tropical to subtropical carbonate systems; in contrast, thick tropical freshwater peats have accumulated in siliclastic systems. Kalo Formation coals, which we interpret as freshwater deposits, formed in siliciclastic depositional settings, similar to those of modern tropical freshwater peat, and to other Pennsylvanian coals in North America interpreted as freshwater deposits. In the late Atokan and earliest Desmoinesian (mid-Moscovian), cordaiteans and tree ferns predominated in the Western Interior and Illinois Basins; lycopsids and cordaiteans predominated in the Appalachian and Donets Basins. The scarcity of lycopsid-only mires in North America during the late Atokan–earliest Desmoinesian (mid-Moscovian) suggests drier climates than during the mid-to-late Desmoinesian (late Moscovian). Rather than indicating mangrove swamps, cordaite-dominated peat may indicate climates with a ‘low-rain’ season. Although most plants in cordaite-dominated peat probably grew in freshwater, coastal mires in climate zones with seasons of ‘low-rain’ may harbor mangrove taxa. The Changuinola Swamp of Panama, a modern peat-accumulating wetland that has a ‘low-rain’ season, is a possible analog of ancient cordaite-dominated mires. In Changuinola, most plants require freshwater; however mangroves, sustained by salt-water influx into the swamp, grow along the seaward edge and along blackwater creeks. The ‘low-rain’ season hypothesis has implications for understanding rainfall amount and continuity during Pennsylvanian cyclothem deposition. The floral succession in diverse cordaite coals, from cordaiteans to tree ferns to lycopsids, suggests increasingly wet climate during coal accumulation. The position of these coals immediately above the sequence boundary suggests humid climate during early glacial melting for these cyclothems.