Summary phylogenetic hypothesis of the Echinodermata, based on David and Mooi (1997), Littlewood et al. (1997), and Sumrall and Sprinkle (1997). Note that the phylogenetic position of most fossil echinoderms is still uncertain, and a number of additional extinct taxa will be added to this tree in the future.

Containing group: Deuterostomia

Introduction

Echinoderms form a well-defined and highly-derived clade of metazoans. They have attracted much attention due to their extensive fossil record, ecological importance in the marine realm, intriguing adult morphology, unusual biomechanical properties, and experimentally manipulable embryos. The approximately 7,000 species of extant echinoderms fall into five well-defined clades: Crinoidea (sea lilies and feather stars), Ophiuroidea (basket stars and brittle stars), Asteroidea (starfishes), Echinoidea (sea urchins, sand dollars, and sea biscuits), and Holothuroidea (sea cucumbers). The phylogenetic position of the Concentricycloidea (sea daisies; 2 species), remains controversial (Baker et al. 1986; Smith 1988b; Pearse and Pearse 1994; Mooi et al. 1997).
Approximately 13,000 echinoderm species are known from the fossil record. All Mesozoic and Cenozoic forms clearly fall into the five extant clades, but the Paleozoic record contains numerous distinct and often bizarre forms that have been placed into approximately 15 additional classes. Phylogenetic relationships, and in some cases status as monophyletic groups, remains unclear for the extinct classes. Unquestionable echinoderms first appear in the fossil record during the mid-Cambrian. Arkarua, a possible echinoderm, has been described from the Vendian (latest Proterozoic) (Gehling 1987).

Characteristics

Synapomorphies of the Echinodermata

Echinoderms are among the most distinctive of all animal phyla. Inclusion in the phylum is readily diagnosable on basis of the four synapomorphies below. Most of these features are present, or can be inferred, even in the earliest fossils. Together, these synapomorphies define much of what makes the functional biology of echinoderms distinctive from that of other metazoans.

1. Calcitic skeleton composed of many ossicles. The biomineral matrix of echinoderm skeletons is composed of calcium carbonate and several proteins. The calcite is deposited as numerous tiny crystals, but all of them lie on the same crystal axis within an ossicle. For this reason, ossicles are birefringent under polarizing light. Ossicles are not solid, but have a sponge-like microstructure called stereom that is unique to the phylum. Embryologically, echinoderm ossicles are a true endoskeleton, since they are produced by mesenchymal cells and are usually covered by epidermis. Functionally, however, the majority of ossicles act more like an exoskeleton, lying just under the epidermis and enclosing most other tissues in a flexible but tough covering.
2. Water vascular system. The water vascular system performs many important functions in echinoderms, including locomotion, respiration, and feeding; in addition, most sensory neurons are located at the termini of podia (tubefeet) which are part of this organ system. The water vascular system may have evolved from simple tentacular systems similar to those in other deuterostome phyla, such as the tentacles of pterobranch hemichordates. However, there are many derived features of the water vascular system in echinoderms, including: an embryological origin from left mesocoel, podia arranged along branches (ambulacra), and a central circumesophageal ring.
3. Mutable collagenous tissue. The ossicles of echinoderms are connected by ligaments composed predominantly of collagen. The material properties of this connective tissue are mutable on short timescales, under neuronal control. Ligaments are normally "locked" (rigid), but can be temporarily "unlocked" (loosened). This provides some interesting mechanical advantages, including the ability to maintain a variety of postures with no muscular effort. In holothuroids, which contain only microscopic ossicles, the entire body wall contains mutable collagenous tissue.
4. Pentaradial body organization in adults. The adults of all extant echinoderms are radially symmetrical. A superficial bilateral organization has evolved twice, in irregular echinoids and holothuroids, but is based on an underlying five-fold organization of skeleton and most organ systems, and is clearly secondary. Higher order radial symmetry (e.g., seven-fold or nine-fold) has evolved on several occasions, and is also clearly a secondary modification. The evolutionary origins of five-fold symmetry remain obscure. Some early Paleozoic echinoderms are not radially symmetrical (e.g., carpoids and helicoplacoids), while a possible echinoderm from the Vendian (Arkarua) has five-fold radial body organization.

Plesiomorphies and other features

1. Marine habit. All extant echinoderms live in the ocean, and there is no fossil evidence of any exception to this. Within the marine realm, echinoderms occupy nearly all habitats, where they often constitute a major proportion of the biomass.
2. Pelago-benthic life cycle. With rare exception, echinoderms are gonochoric (separate sexes) with no overt sexual dimorphism. Fertilization is almost always external. Ancestrally (and still, typically), the life cycle is complex, with a free-living larva that is planktotrophic (grazes on unicellular algae). Larvae are plesiomorphically bilaterally symmetrical, have a recurved gut and transparent ectoderm, and feed by upstream particle capture using the ciliated band. Metamorphosis is typically radical and occurs during settlement onto the benthos.
3. Coelomate. Echinoderms form their coeloms as outpocketings from the archenteron (embryonic gut), a process called enterocoely. In most species, the coeloms are trimerous, and initially bilaterally symmetrical. The fates of the various coelomic compartments vary among echinoderms, but some features seem broadly similar and may reflect a common evolutionary origin deep within the phylum: left mesocoel gives rise to most or all of the water vascular system, and one or both somatocoels form the lining of the body cavity.
4. Deuterostome. Like some related phyla, the blastopore (site where gastrulation begins) in echinoderm embryos becomes the larval anus; the larval mouth is a secondary opening. In some extant forms, the larval mouth is preserved as the adult mouth, while in others the entire digestive system is re-plumbed during metamorphosis and a new mouth and anus form.
5. Simple hemal/excretory system. The hemal and excretory systems of echinoderms are linked into what Nielsen (1996) calls the "axial complex". This organ system shows similarities, and may be homologous, to those of other deuterostome phyla. In echinoderms, it is composed of: a thickened vessel (the "heart") lacking an endothelium and surrounded by a pericardium; a region where ultrafiltration occurs via podocytes; a closed circulatory system; and an opening to the external environment called the madreporite.
6. Decentralized nervous system. The arrangment of the central nervous sytem of echinoderms is quite different from that in other deuterostomes. Radial nerves run under each of the ambulacra, and contain the cell bodies of almost all motor neurons and interneurons. A central nerve ring surrounds the gut, and is composed primarily of fiber tracks connecting the radial nerves. No known echinoderm contains anything that could be called a brain, although ganglia are present along the radial nerves in some echinoderms. Unlike most bilaterian phyla, echinoderms lack any trace of cephalization, and have no specialized sense organs. Sensory neurons are located primarily within the ectoderm of podia, and send axons to the radial nerves.

Discussion of Phylogenetic Relationships

With the possible exception of two species, all extant echinoderms fall into five well-defined clades, traditionally ranked as Classes: the Crinoidea, Asteroidea, Ophiuroidea, Echinoidea, and Holothuroidea. The monophyly of these Classes is not in serious doubt. The phylogenetic position of two species, however, remains unresolved at the Class level. Both species belong to the recently-described "sixth" class, the Concentricycloidea; they may be highly derived asteroids, perhaps related to caymanostellids (Baker et al. 1986; Smith 1988b), but this remains controversial (Pearse 1994; Mooi et al. 1997).
Phylogenetic relationships among the five extant classes have been the subject of considerable debate. Renewed interest in resolving this problem during the past decade has greatly narrowed the number of likely topologies (Littlewood et al. 1997). It is generally agreed that the lineage leading to the Crinoidea branched most basally, and that the Echinoidea and Holothuroidea are extant sister clades. Debate now centers on whether the Ophiuroidea and Asteroidea form a clade. The two best-supported hypotheses are:
The "Asterozoan" hypothesis was first proposed by Bather (1900), and has recently been supported by the work of Mooi and David (1997). The alternative hypothesis dates back to MacBride (1906). More recently, (Smith 1988a) advocated the same topology, and proposed the name Cryptosyringida for the clade (Ophuroidea + Echinoidea + Holothuroidea). These two hypotheses are preferred, to a nearly equal degree, by molecular analyses (18S and 26S rRNA sequences) and "total evidence" analyses (summarized in Littlewood et al. 1997). Mitochondrial gene order seems to support the Asterozoan hypothesis (Smith et al. 1993), but information from crinoids is needed to clarify the polarity of the character transformations.
Including fossil taxa, the number of echinoderm classes rises to approximately 20. The lack of a clear understanding of homologies among ossicles in various extinct classes has hampered attempts to reconstruct their phylogenetic relationships (Mooi and David 1997), and it is fair to say that much work remains to be done. Analyses by Smith and Paul (1984), Smith (1988a), and Sumrall and Sprinkle (1997) are the most comprehensive and rigorous available for Paleozoic echinoderms.

Other Names for Echinodermata

• Vernacular Names: echinoderms, spiny-skinned animals

Summary phylogenetic hypothesis of the Echinodermata, based on David and Mooi (1997), Littlewood et al. (1997), and Sumrall and Sprinkle (1997). Note that the phylogenetic position of most fossil echinoderms is still uncertain, and a number of additional extinct taxa will be added to this tree in the future.

Containing group: Deuterostomia

Introduction

Echinoderms form a well-defined and highly-derived clade of metazoans. They have attracted much attention due to their extensive fossil record, ecological importance in the marine realm, intriguing adult morphology, unusual biomechanical properties, and experimentally manipulable embryos. The approximately 7,000 species of extant echinoderms fall into five well-defined clades: Crinoidea (sea lilies and feather stars), Ophiuroidea (basket stars and brittle stars), Asteroidea (starfishes), Echinoidea (sea urchins, sand dollars, and sea biscuits), and Holothuroidea (sea cucumbers). The phylogenetic position of the Concentricycloidea (sea daisies; 2 species), remains controversial (Baker et al. 1986; Smith 1988b; Pearse and Pearse 1994; Mooi et al. 1997).
Approximately 13,000 echinoderm species are known from the fossil record. All Mesozoic and Cenozoic forms clearly fall into the five extant clades, but the Paleozoic record contains numerous distinct and often bizarre forms that have been placed into approximately 15 additional classes. Phylogenetic relationships, and in some cases status as monophyletic groups, remains unclear for the extinct classes. Unquestionable echinoderms first appear in the fossil record during the mid-Cambrian. Arkarua, a possible echinoderm, has been described from the Vendian (latest Proterozoic) (Gehling 1987).

Characteristics

Synapomorphies of the Echinodermata

Echinoderms are among the most distinctive of all animal phyla. Inclusion in the phylum is readily diagnosable on basis of the four synapomorphies below. Most of these features are present, or can be inferred, even in the earliest fossils. Together, these synapomorphies define much of what makes the functional biology of echinoderms distinctive from that of other metazoans.

1. Calcitic skeleton composed of many ossicles. The biomineral matrix of echinoderm skeletons is composed of calcium carbonate and several proteins. The calcite is deposited as numerous tiny crystals, but all of them lie on the same crystal axis within an ossicle. For this reason, ossicles are birefringent under polarizing light. Ossicles are not solid, but have a sponge-like microstructure called stereom that is unique to the phylum. Embryologically, echinoderm ossicles are a true endoskeleton, since they are produced by mesenchymal cells and are usually covered by epidermis. Functionally, however, the majority of ossicles act more like an exoskeleton, lying just under the epidermis and enclosing most other tissues in a flexible but tough covering.
2. Water vascular system. The water vascular system performs many important functions in echinoderms, including locomotion, respiration, and feeding; in addition, most sensory neurons are located at the termini of podia (tubefeet) which are part of this organ system. The water vascular system may have evolved from simple tentacular systems similar to those in other deuterostome phyla, such as the tentacles of pterobranch hemichordates. However, there are many derived features of the water vascular system in echinoderms, including: an embryological origin from left mesocoel, podia arranged along branches (ambulacra), and a central circumesophageal ring.
3. Mutable collagenous tissue. The ossicles of echinoderms are connected by ligaments composed predominantly of collagen. The material properties of this connective tissue are mutable on short timescales, under neuronal control. Ligaments are normally "locked" (rigid), but can be temporarily "unlocked" (loosened). This provides some interesting mechanical advantages, including the ability to maintain a variety of postures with no muscular effort. In holothuroids, which contain only microscopic ossicles, the entire body wall contains mutable collagenous tissue.
4. Pentaradial body organization in adults. The adults of all extant echinoderms are radially symmetrical. A superficial bilateral organization has evolved twice, in irregular echinoids and holothuroids, but is based on an underlying five-fold organization of skeleton and most organ systems, and is clearly secondary. Higher order radial symmetry (e.g., seven-fold or nine-fold) has evolved on several occasions, and is also clearly a secondary modification. The evolutionary origins of five-fold symmetry remain obscure. Some early Paleozoic echinoderms are not radially symmetrical (e.g., carpoids and helicoplacoids), while a possible echinoderm from the Vendian (Arkarua) has five-fold radial body organization.

Plesiomorphies and other features

1. Marine habit. All extant echinoderms live in the ocean, and there is no fossil evidence of any exception to this. Within the marine realm, echinoderms occupy nearly all habitats, where they often constitute a major proportion of the biomass.
2. Pelago-benthic life cycle. With rare exception, echinoderms are gonochoric (separate sexes) with no overt sexual dimorphism. Fertilization is almost always external. Ancestrally (and still, typically), the life cycle is complex, with a free-living larva that is planktotrophic (grazes on unicellular algae). Larvae are plesiomorphically bilaterally symmetrical, have a recurved gut and transparent ectoderm, and feed by upstream particle capture using the ciliated band. Metamorphosis is typically radical and occurs during settlement onto the benthos.
3. Coelomate. Echinoderms form their coeloms as outpocketings from the archenteron (embryonic gut), a process called enterocoely. In most species, the coeloms are trimerous, and initially bilaterally symmetrical. The fates of the various coelomic compartments vary among echinoderms, but some features seem broadly similar and may reflect a common evolutionary origin deep within the phylum: left mesocoel gives rise to most or all of the water vascular system, and one or both somatocoels form the lining of the body cavity.
4. Deuterostome. Like some related phyla, the blastopore (site where gastrulation begins) in echinoderm embryos becomes the larval anus; the larval mouth is a secondary opening. In some extant forms, the larval mouth is preserved as the adult mouth, while in others the entire digestive system is re-plumbed during metamorphosis and a new mouth and anus form.
5. Simple hemal/excretory system. The hemal and excretory systems of echinoderms are linked into what Nielsen (1996) calls the "axial complex". This organ system shows similarities, and may be homologous, to those of other deuterostome phyla. In echinoderms, it is composed of: a thickened vessel (the "heart") lacking an endothelium and surrounded by a pericardium; a region where ultrafiltration occurs via podocytes; a closed circulatory system; and an opening to the external environment called the madreporite.
6. Decentralized nervous system. The arrangment of the central nervous sytem of echinoderms is quite different from that in other deuterostomes. Radial nerves run under each of the ambulacra, and contain the cell bodies of almost all motor neurons and interneurons. A central nerve ring surrounds the gut, and is composed primarily of fiber tracks connecting the radial nerves. No known echinoderm contains anything that could be called a brain, although ganglia are present along the radial nerves in some echinoderms. Unlike most bilaterian phyla, echinoderms lack any trace of cephalization, and have no specialized sense organs. Sensory neurons are located primarily within the ectoderm of podia, and send axons to the radial nerves.

Discussion of Phylogenetic Relationships

With the possible exception of two species, all extant echinoderms fall into five well-defined clades, traditionally ranked as Classes: the Crinoidea, Asteroidea, Ophiuroidea, Echinoidea, and Holothuroidea. The monophyly of these Classes is not in serious doubt. The phylogenetic position of two species, however, remains unresolved at the Class level. Both species belong to the recently-described "sixth" class, the Concentricycloidea; they may be highly derived asteroids, perhaps related to caymanostellids (Baker et al. 1986; Smith 1988b), but this remains controversial (Pearse 1994; Mooi et al. 1997).
Phylogenetic relationships among the five extant classes have been the subject of considerable debate. Renewed interest in resolving this problem during the past decade has greatly narrowed the number of likely topologies (Littlewood et al. 1997). It is generally agreed that the lineage leading to the Crinoidea branched most basally, and that the Echinoidea and Holothuroidea are extant sister clades. Debate now centers on whether the Ophiuroidea and Asteroidea form a clade. The two best-supported hypotheses are:
The "Asterozoan" hypothesis was first proposed by Bather (1900), and has recently been supported by the work of Mooi and David (1997). The alternative hypothesis dates back to MacBride (1906). More recently, (Smith 1988a) advocated the same topology, and proposed the name Cryptosyringida for the clade (Ophuroidea + Echinoidea + Holothuroidea). These two hypotheses are preferred, to a nearly equal degree, by molecular analyses (18S and 26S rRNA sequences) and "total evidence" analyses (summarized in Littlewood et al. 1997). Mitochondrial gene order seems to support the Asterozoan hypothesis (Smith et al. 1993), but information from crinoids is needed to clarify the polarity of the character transformations.
Including fossil taxa, the number of echinoderm classes rises to approximately 20. The lack of a clear understanding of homologies among ossicles in various extinct classes has hampered attempts to reconstruct their phylogenetic relationships (Mooi and David 1997), and it is fair to say that much work remains to be done. Analyses by Smith and Paul (1984), Smith (1988a), and Sumrall and Sprinkle (1997) are the most comprehensive and rigorous available for Paleozoic echinoderms.

Other Names for Echinodermata

• Vernacular Names: echinoderms, spiny-skinned animals

Phylogeny modified from James et al., 2006a, 2006b; Liu et al., 2006; Seif et al., 2005; Steenkamp et al., 2006.

Containing group: Eukaryotes

Introduction

The organisms of the fungal lineage include mushrooms, rusts, smuts, puffballs, truffles, morels, molds, and yeasts, as well as many less well-known organisms (Alexopoulos et al., 1996). More than 70,000 species of fungi have been described; however, some estimates of total numbers suggest that 1.5 million species may exist (Hawksworth, 1991; Hawksworth et al., 1995).
As the sister group of animals and part of the eukaryotic crown group that radiated about a billion years ago, the fungi constitute an independent group equal in rank to that of plants and animals. They share with animals the ability to export hydrolytic enzymes that break down biopolymers, which can be absorbed for nutrition. Rather than requiring a stomach to accomplish digestion, fungi live in their own food supply and simply grow into new food as the local environment becomes nutrient depleted.
Most biologists have seen dense filamentous fungal colonies growing on rich nutrient agar plates, but in nature the filaments can be much longer and the colonies less dense. When one of the filaments contacts a food supply, the entire colony mobilizes and reallocates resources to exploit the new food. Should all food become depleted, sporulation is triggered. Although the fungal filaments and spores are microscopic, the colony can be very large with individuals of some species rivaling the mass of the largest animals or plants.
Prior to mating in sexual reproduction, individual fungi communicate with other individuals chemically via pheromones. In every phylum at least one pheromone has been characterized, and they range from sesquiterpines and derivatives of the carotenoid pathway in chytridiomycetes and zygomycetes to oligopeptides in ascomycetes and basidiomycetes.
Within their varied natural habitats fungi usually are the primary decomposer organisms present. Many species are free-living saprobes (users of carbon fixed by other organisms) in woody substrates, soils, leaf litter, dead animals, and animal exudates. The large cavities eaten out of living trees by wood-decaying fungi provide nest holes for a variety of animals, and extinction of the ivory billed woodpecker was due in large part to loss, through human activity, of nesting trees in bottom land hardwoods. In some low nitrogen environments several independent groups of fungi have adaptations such as nooses and sticky knobs with which to trap and degrade nematodes and other small animals. A number of references on fungal ecology are available (Carroll and Wicklow, 1992; Cooke and Whipps, 1993; Dix and Webster, 1995).
However, many other fungi are biotrophs, and in this role a number of successful groups form symbiotic associations with plants (including algae), animals (especially arthropods), and prokaryotes. Examples are lichens, mycorrhizae, and leaf and stem endophytes. Although lichens may seem infrequent in polluted cities, they can form the dominant vegetation in nordic environments, and there is a better than 80% chance that any plant you find is mycorrhizal. Leaf and stem endophytes are a more recent discovery, and some of these fungi can protect the plants they inhabit from herbivory and even influence flowering and other aspects of plant reproductive biology. Fungi are our most important plant pathogens, and include rusts, smuts, and many ascomycetes such as the agents of Dutch elm disease and chestnut blight. Among the other well known associations are fungal parasites of animals. Humans, for example, may succumb to diseases caused by Pneumocystis (a type of pneumonia that affects individuals with supressed immune systems), Coccidioides (valley fever), Ajellomyces (blastomycosis and histoplasmosis), and Cryptococcus (cryptococcosis) (Kwon-Chung and Bennett, 1992).
Fungal spores may be actively or passively released for dispersal by several effective methods. The air we breathe is filled with spores of species that are air dispersed. These usually are species that produce large numbers of spores, and examples include many species pathogenic on agricultural crops and trees. Other species are adapted for dispersal within or on the surfaces of animals (particularly arthropods). Some fungi are rain splash or flowing water dispersed. In a few cases the forcible release of spores is sufficient to serve as the dispersal method as well. The function of some spores is not primarily for dispersal, but to allow the organisms to survive as resistant cells during periods when the conditions of the environment are not conducive to growth.
Fungi are vital for their ecosystem functions, some of which we have reviewed in the previous paragraphs. In addition a number of fungi are used in the processing and flavoring of foods (baker's and brewer's yeasts, Penicillia in cheese-making) and in production of antibiotics and organic acids. Other fungi produce secondary metabolites such as aflatoxins that may be potent toxins and carcinogens in food of birds, fish, humans, and other mammals.
A few species are studied as model organisms that can be used to gain knowledge of basic processes such as genetics, physiology, biochemistry, and molecular biology with results that are applicable to many organisms (Taylor et al., 1993). Some of the fungi that have been intensively studied in this way include Saccharomyces cereviseae, Neurospora crassa, and Ustilago maydis.
Most phyla appear to be terrestrial in origin, although all major groups have invaded marine and freshwater habitats. An exception to this generality is the flagellum-bearing phyla Chytridiomycota, Blastocladiomycota, and Neocallimastigomycota (collectively referred to as chytrids), which probably had an aquatic origin. Extant chytrid species also occur in terrestrial environments as plant pathogenic fungi, soil fungi, and even as anaerobic inhabitants of the guts of herbivores such as cows (all Neocallimastigomycota).

Characteristics

Fungi are characterized by non-motile bodies (thalli) constructed of apically elongating walled filaments (hyphae), a life cycle with sexual and asexual reproduction, usually from a common thallus, haploid thalli resulting from zygotic meiosis, and heterotrophic nutrition. Spindle pole bodies, not centrioles, usually are associated with the nuclear envelope during cell division. The characteristic wall components are chitin (beta-1,4-linked homopolymers of N-acetylglucosamine in microcrystalline state) and glucans primarily alpha-glucans (alpha-1,3- and alpha-1,6- linkages) (Griffin, 1994).
Exceptions to this characterization of fungi are well known, and include the following: Most species of chytrids have cells with a single, smooth, posteriorly inserted flagellum at some stage in the life cycle, and centrioles are associated with nuclear division. The life cycles of most chytrids are poorly studied, but some (Blastocladiomycota) are known to have zygotic meiosis (therefore, alternation between haploid and diploid generations). Certain members of Mucoromycotina, Ascomycota, and Basidiomycota may lack hyphal growth during part or all of their life cycles, and, instead, produce budding yeast cells. Most fungal species with yeast growth forms contain only minute amounts of chitin in the walls of the yeast cells. A few species of Ascomycota (Ophiostomataceae) have cellulose in their walls, and certain members of Blastocladiomycota and Entomophthoromycotina lack walls during part of their life cycle (Alexopoulos et al., 1996).

Fossil Record

Based on the available fossil record, fungi are presumed to have been present in Late Proterozoic (900-570 mya). Terrestrial forms of purported ascomycetes are reported in associations with microarthropods in the Silurian Period (438-408 mya) (Sherwood-Pike and Gray, 1985). Fossil hyphae in association with wood decay and fossil chytrids and Glomales-Endogonales representatives associated with plants of the Rhynie Chert are reported from the Devonian Period (408-360 mya) (Hass et al., 1994; Remy et al., 1994a, 1994b; Taylor et al., 1994a, 1995b). Fungal fossil diversity increased throughout the Paleozoic Era (Taylor et al., 1994b) with all modern classes reported in the Pennsylvanian Epoch (320-286 mya).
A first attempt to match molecular data on fungal phylogeny to the geological record shows general agreement, but does point out some conflicts between the two types of data (Berbee and Taylor 1993).

Biogeography

Wherever adequate moisture, temperature, and organic substrates are available, fungi are present. Although we normally think of fungi as growing in warm, moist forests, many species occur in habitats that are cold, periodically arid, or otherwise seemingly inhospitable. It is important to recognize that optimum conditions for growth and reproduction vary widely with fungal species. Diversity of most groups of fungi tends to increase in tropical regions, but detailed studies are only in their infancy (Isaac et al., 1993).
Although many saprobic and plant pathogenic species with low substrate specificity and effective dispersal systems have broad distributions, gene flow appears to be restricted in many fungi. For these species large bodies of water such as the Atlantic and Pacific Oceans create barriers to gene exchange. Some distributions are limited by substrate availability, and dramatic examples come from parasites of Gondowanan plants; one of these is the Southern Hemisphere distribution of the ascomycete Cyttaria, corresponding with part of the distribution of its host plant Nothofagus. The fossil record shows that fungi were present in Antarctica, as is the case for other organisms with Gondwanan distributions. Arthropod associates also may show distributions throughout part or all of a host range, and some fungal species (ex. wood wasp associates) occur outside the range of the associated arthropod.

Notable Fungi

• The largest known basidioma (mushroom or fruiting body) was that of a Rigidioporus ulmarius (Agaricomycetes), hidden-away in a shady corner of the Royal Botanic Gardens, Kew, Richmond, Surrey, England. This fruiting body was mentioned in the Guinness Book of World Records (Matthews, 1994). At the beginning of every New Year the Annual Mensuration Ceremony of the fruiting body took place, and on 19 January 1996 it had increased to 170 cm maximum length (up from 159 in 1995) and 146 cm maximum width (up from 140 in 1995). It also grew 4 cm taller from the soil level, measuring 54 cm. The weight of the fruiting body was estimated to be 284 kg (625 pounds)! Amid rumors of its destruction, Dr. Brian M. Spooner, Head of Mycology, Royal Botanic Gardens, has brought us up to date on the fate of the record specimen. Unfortunately, the basidioma began to rot at the edges a few years ago, likely because the hyphal body of the fungus digested away its elm root substrate, reminding us that a fungus needs a good dispersal system to escape the substrate that eventually inevitably is destroyed. In the life of the fruiting body many trillions of spores must have been produced, and some of these surely fell on an appropiate substrate to establish a new infection. The final insult to the fruiting body came from a fox that burrowed under one side and caused it to collapse.
  

  Click on an image to view larger version & data in a new window

  Figure 6: The largest basidioma world record holder Rigidioporus ulmarius at Kew when it was still intact. The mushroom is shown in its largest dimension (170 cm or over 5 ¹/₂ feet). Copyright © D. Pegler 1996.
  
  Other large basidiomata are those of a Canadian puffball almost 9 feet in circumference (over 48 pounds) and a basidiocarp of the sulfur mushroom in England (100 pounds). A previous Guinness Book of World Records record-sized fruiting body of Bridgeoporus nobilissimus, an endangered species of the Pacific Northwest of the United States, is over 160 kg (300 pounds) and may have regained the title of “largest” with the demise of the Kew specimen. This polypore also may do itself in because its great weight is likely to eventually cause it to fall as the mycelium depletes its food source, often the noble fir tree.
• Reproductive structures clearly can be very large, but what about the body of the fungus, which often is hidden from view within the substrate? One fungus body constructed of tubular filaments (hyphae) was brought to our attention when molecular techniques were used to show that it was extensive (37 acres and an estimated blue whale equivalent size of 110 tons). The Michigan fungus clone (Armillaria bulbosa, Agaricomycetes) grew in tree roots and soil. This report drew attention to an even larger fungal clone of Armillaria ostoyae, reported earlier in the state of Washington, which covered over 1,500 acres. Each clone began from the germination of a single spore over a thousand years ago. Although they probably have fragmented and are no longer continuous bodies, such organisms give us cause to think about what constitutes an individual.
• Penicillium chrysogenum (Ascomycota) is known for its production of the antibiotic penicillin. Although other antibiotics are produced by a variety of organisms, penicillin was the first to be developed. In the spring of 1996 a long dried out culture of the original isolate prepared by its discoverer, Sir Alexander Fleming in the late 1920s, was auctioned by Sotheby's of London and sold to a pharmaceutical company for 23,000 pounds. This price is insignificant when one considers the worth of this fungus, not only in sales of penicillin, but in terms of illnesses cured and lives saved. In the past a simple scratch or blister sometimes could result in a fatal infection such as the blister that resulted in the death of John Calvin Coolidge (1918-1924), the son of a U. S. president. However, misuse of penicillin and other antibiotics has resulted in selection of resistant microorganisms, and the threat of untreatable bacterial infections and diseases (for example Staphylococcus aureus and Escherichia coli and tuberculosis and syphilis) is still present in our homes and recreation areas.
• Fungal spores fill the air we breathe. On many days in some localities the number of fungal spores in the air far exceeds the pollen grains. Fungal spores also cause allergies; however, unlike seasonal pollen production, some fungi can produce spores all year long. The largest number of fungal spores ever sampled was over 5.5 million per cubic foot in Wales (Matthews, 1994).
• Basidiomycetes have always attracted a lot of attention because some of them have large basidiocarps, but the realization that all fungi are important in ecosystem function has drawn more attention to microscopic forms as well. For example a report on the secret sex life of a yeast-like ascomycete human pathogen, Coccidioides immitis, made a headline of the New York Times (6 February 1996, p. B7). This fungus causes Valley Fever and is endemic in parts of the southwestern United States. Although no one has been able to observe sexual reproduction in this species, molecular studies show genetic diversity that is best explained by occurrence of sexual reproduction in the life cycle.
• Another yeast-like ascomycete reported in the Dallas Morning News (28 August 1995, p. 8D) lives in the gut of cigar beetles and is essential to the beetle's health. Without the gut fungi to detoxify the plant material of toxins, the beetles would be poisoned. Keep on the lookout for other reports of fascinating fungal feats.

Discussion of Phylogenetic Relationships

The kingdom Fungi is a diverse clade of heterotrophic organisms that shares some characters with animals such as chitinous structures, storage of glycogen, and mitochondrial codon UGA encoding tryptophan. Both animals and fungi have spores or gametes with a single smooth, posteriorly inserted flagellum, but only species of the basal chytrid phyla have retained this primitive character (Barr, 1992; Cavalier-Smith, 1987, 1995). Fungi, animals, and other heterotrophic protist-like organisms such as choanoflagellates and Mesomycetozoea are now considered part of the larger group termed opisthokonts (Cavalier-Smith, 1987) in reference to the posterior flagellum.
The branch uniting the fungi and animals is well-supported based on a number of molecular phylogenetic datasets, including the nuclear small subunit ribosomal RNA gene (Wainwright et al., 1993; Bruns et al. 1993), unique and shared sequence insertions in proteins such as elongation factor 1α (Baldauf and Palmer, 1993), entire mitochondrial genomes (Lang et al., 2002), and concatenated protein-coding genes (Steenkamp et al., 2006).
Prior classification systems of Fungi based primarily on morphology are in need of updating to more accurately reflect phylogenetic relationships as determined by molecular systematics. Molecular characters have been essential for phylogenetic analysis in cases when morphological characters are convergent, reduced, or missing among the taxa considered. This is especially true of species that never reproduce sexually, because characters of sexual reproduction traditionally have been the basis for classification of Fungi. Use of molecular characters allows asexual fungi to be placed among their closest relatives.
Previous classifications placed early-diverging fungal groups (non-Ascomycota or Basidiomycota) into two phyla: Chytridiomycota and Zygomycota. Numerous phylogenetic studies now suggest that neither is monophyletic, and the latest classification scheme includes six phyla and an additional four unplaced subphyla (Hibbett et al., 2007). At present, because of the ancient divergence times between the fungal phyla, the exact phylogenetic relationships are ambiguous. Chytrids appear to be a paraphyletic group at the base of the fungal phylogeny and merely fungal lineages which have retained the character of flagellated spores. Three phyla of flagellated fungi are proposed (Blastocladiomycota, Chytridiomycota, and Neocallimastigomycota; Hibbett et al., 2007) and two chytrid genera Olpidium and Rozella, are of uncertain phylogenetic position (James et al., 2006a, 2006b). These genera are interesting because they are both highly reduced endoparasites (living inside the host cell) whose entire thallus consists of only a spherical body absorbing nutrients from the host material that surrounds it. Rozella appears in an isolated position in the fungal phylogeny as the very earliest lineage to diverge from the rest of the fungi (James et al., 2006a, 2006b). In contrast, Olpidium brassicae appears to have diverged after the majority of chytrids and is more closely related to some zygomycete fungi (James et al., 2006a, 2006b).
Fungi with non-septate or irregularly septate hyphae and thick-walled spores were traditionally placed in the phylum Zygomycota. However, evidence for a monophyletic Zygomycota is lacking (Seif et al., 2005), and the deconstruction of the Zygomycota into four unordered subphyla (Entomophthoromycotina, Kickxellomycotina, Mucoromycotina, Zoopagomycotina) has been proposed (Hibbett et al., 2007). The separation of the superficially similar arbuscular mycorrhizal fungi (that lack septa in hyphae but also lack zygospores) into the phylum Glomeromycota has been previously proposed (Schüßler et al., 2001). Whether this phylum is more closely related to the Ascomycota and Basidiomycota lineage or to other zygomycete lineages is controversial (Redecker et al., 2006).
Evidence from shared morphological characters such as regularly septate hyphae and a dikaryotic stage (two separate and different nuclei in a single hyphal segment) in the life cycle usually has been interpreted as support for a close relationship between Basidiomycota and Ascomycota. Numerous phylogenetic studies such as SSU rDNA (Berbee and Taylor, 1992), RNA polymerase genes (Liu et al., 2006), and mitochondrial genome sequencing (Seif et al., 2005) provide strong support for this relationship. A subkingdom termed Dikarya is proposed (Hibbett et al., 2007), creating a division between a highly speciose subkingdom (Dikarya) and the remaining early diverging lineages whose relationships are not precisely known.
Fungal classification is far from static, and even which organisms are actually members of Fungi is changing. For example, the group trichomycetes describes gut inhabitants of arthropods that share similarities with zygomycetes. Molecular phylogenetic studies have demonstrated that two of the four orders of trichomycetes are actually members of the Mesomycetozoea protist group (Benny and O’Donnell, 2000; Cafaro, 2005). Other organisms that were previously considered to be Fungi because of their heterotrophic, mold-like growth forms are now classified as stramenopiles (Oomycota, Hyphochytriomycota, and Labyrinthulomycota) or slime molds (Myxomycota, Plasmodiomycota, Dictyosteliomycota, Acrasiomycota) (Bhattacharya et al., 1992; Leipe et al., 1994; Van der Auwera et al., 1995). More interesting for mycologists are the findings that some species previously considered protozoa are actually Fungi. For example, the species Hyaloraphidium curvatum was assumed to be a green alga that had adopted a heterotrophic lifecycle concomitantly with losing its chloroplast. It is now known to be a chytrid fungus related to Monoblephariomycetes but lacking a flagellated stage (Ustinova et al., 2000). Other examples include the parasitic organisms presumed to be protozoa, such as the cockroach parasite Nepridiophaga (Wylezich et al., 2004) and the Daphnia parasite Polycarum (Johnson et al., 2006) recently demonstrated to be members of the fungal kingdom based on SSU rDNA phylogenies.
The most revolutionary addition to the fungal lineage has occurred with phylogenetic evidence indicating the protist group microsporidia is closely related to Fungi–possibly derived from zygomycetes (Keeling, 2003) or sister to the genus Rozella on the earliest branch in the fungal kingdom (James et al., 2006a). Microsporidia are highly specialized intracellular parasites (primarily of animals) that lack mitochondria but have chitin and trehalose in their spores (similar to Fungi). All molecular studies have shown that microsporidia evolve at an extremely accelerated rate of evolution, making their placement in the Tree of Life difficult. The relationship with fungi is supported by many single and multiple gene phylogenies (e.g., Liu et al., 2006), but an exact placement within the fungi has not received strong support (Keeling and Fast, 2002).
More recently the nuclearid amoebae have been demonstrated to be a sister group to the Fungi with strong support (Steenkamp et al., 2006). This finding is significant because Nuclearia lacks a cell wall and has phagotrophic nutrition in which the food source (such as a bacterium or algal cell) is engulfed wholly, unlike fungi and microsporidia which utilize absorptive nutrition. Further sampling of basal fungal lineages will be needed to determine whether a Nuclearia-like organism was the cenancestor (most recent common ancestor) of Fungi.

Other Names for Fungi

• Mycota
• Eumycota