A Explanations of Important Terms And Concepts
A.1 Autotrophs and Heterotrophs
An autotroph (“self-feeding”, from the Greek autos “self” and trophe “nourishing”) or producer, is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) from simple substances present in its surroundings, generally using energy from light (photosynthesis) or inorganic chemical reactions (chemosynthesis). They are the producers in a food chain, such as plants on land or algae in water. Autotrophs can reduce carbon dioxide to make organic compounds for biosynthesis and also create a store of chemical energy. Most autotrophs use water as the reducing agent, but some can use other hydrogen compounds such as hydrogen sulfide.
Autotrophs can be photoautotrophs or chemoautotrophs. Phototrophs use light as an energy source, while chemotrophs use electron donors as a source of energy, whether from organic or inorganic sources; however, in the case of autotrophs, these electron donors come from inorganic chemical sources. Such chemotrophs are lithotrophs. Lithotrophs use inorganic compounds, such as hydrogen sulfide, elemental sulfur, ammonium and ferrous iron, as reducing agents for biosynthesis and chemical energy storage. Photoautotrophs and lithoautotrophs use a portion of the ATP produced during photosynthesis or the oxidation of inorganic compounds to reduce NADP+ to NADPH to form organic compounds.
A heterotroph Greek héteros = “other” plus trophe = “nutrition”) is an organism that ingests or absorbs organic carbon (rather than fix carbon from inorganic sources such as carbon dioxide) in order to be able to produce energy and synthesize compounds to maintain its life. Ninety-five percent or more of all types of living organisms are heterotrophic, including all animals and fungi and some bacteria and protists.
Detritivores are heterotrophs which obtain nutrients by consuming detritus (decomposing plant and animal parts as well as feces). Saprotrophs (also called lysotrophs) are chemoheterotrophs that use extracellular digestion in processing decayed organic matter. It is a term most often associated with fungi. The process is most often facilitated through the active transport of such materials through endocytosis within the internal mycelium and its constituent hyphae.
A.2 Biological life cycle
A biological life cycle is a series of changes in form that an organism undergoes, returning to the starting state. Transitions of form may involve growth, asexual reproduction, or sexual reproduction. In some organisms, different “generations” of the species succeed each other during the life cycle. For plants and many algae, there are two multicellular stages, and the life cycle is referred to as alternation of generations. Life cycles that include sexual reproduction involve alternating haploid (n) and diploid (2n) stages, i.e., a change of ploidy is involved. To return from a diploid stage to a haploid stage, meiosis must occur. In regard to changes of ploidy, there are 3 types of life cycles that we will encounter in this course:
- haplontic life cycle (e.g. in fungi): the haploid stage is multicellular and the diploid stage is a single cell, meiosis is “zygotic”.
- diplontic life cycle (e.g. in animals): the diploid stage is multicellular and haploid gametes are formed, meiosis is “gametic”.
- haplodiplontic life cycle (e.g. in plants): multicellular diploid (e.g. the sporophyte in plants) and haploid stages (e.g. the gametophyte in plants) occur, meiosis is “sporic”.
The cycles differ in when mitosis (growth) occurs. Zygotic meiosis and gametic meiosis have one mitotic stage: mitosis occurs during the n (haploid) phase in zygotic meiosis (e.g. in fungi) and during the 2n (diploid) phase in gametic meiosis (e.g. in animals). Therefore, zygotic and gametic meiosis are collectively termed haplobiontic (single mitotic phase, not to be confused with haplontic). Sporic meiosis (e.g. in plants), on the other hand, has mitosis in two stages, both the diploid and haploid stages, termed diplobiontic (not to be confused with diplontic).
A.3 Asexual and Sexual Reproduction
Reproduction (or procreation or breeding) is the biological process by which new individual organisms – “offspring” – are produced from their “parents”. Reproduction is a fundamental feature of all known life; each individual organism exists as the result of reproduction. There are two forms of reproduction: asexual and sexual.
Asexual reproduction is a process by which organisms create genetically similar or identical copies of themselves without the contribution of genetic material from another organism.
Sexual reproduction creates a new organism by combining the genetic material of two organisms. Most animals and plants reproduce sexually. Each of two parent organisms contributes half of the offspring’s genetic makeup by creating haploid gametes. Most organisms form two different types of gametes. In these anisogamous species, the two sexes are referred to as male (producing sperm or microspores) and female (producing ova or megaspores). In isogamous species, the gametes are similar or identical in form (isogametes). Because both gametes look alike, they cannot be classified as “male” or “female.” Instead, organisms undergoing isogamy are said to have different mating types, most commonly noted as “+” and “−” strains. Sexual reproduction in fungi differs in many aspects from sexual reproduction in animals or plants. Sexually compatible fungi combine by fusing their hyphae together. Many fungi go through a dikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells. Sexually reproducing organisms have different sets of genes for every trait (called alleles). Offspring inherit one allele for each trait from each parent. Thus, offspring have a combination of the parents’ genes.
Multicellular organisms are organisms that consist of more than one cell, in contrast to unicellular organisms. Multicellularity allows an organism to exceed the size limits normally imposed by diffusion: single cells with increased size have a decreased surface-to-volume ratio and have difficulty absorbing sufficient nutrients and transporting them throughout the cell. Multicellular organisms thus have the competitive advantages of an increase in size without its limitations. They can have longer lifespans as they can continue living when individual cells die. Multicellularity also permits increasing complexity by allowing differentiation of cell types within one organism. One hypothesis for the origin of multicellularity is that a group of function-specific cells aggregated into a slug-like mass, which moved as a multicellular unit. This is essentially what slime molds do. Another hypothesis is that a primitive cell underwent nucleus division, thereby becoming a coenocyte. A membrane would then form around each nucleus (and the cellular space and organelles occupied in the space), thereby resulting in a group of connected cells in one organism (this mechanism is observable in the fruit fly Drosophila). A third hypothesis is that as a unicellular organism divided, the daughter cells failed to separate, resulting in a conglomeration of identical cells in one organism, which could later develop specialized tissues. This is what plant and animal embryos do as well as colonial choanoflagellates.
In biology, a species is the basic unit of biological classification and a taxonomic rank, as well as a unit of biodiversity. Scientists and others need a species definition which allows them to work, regardless of the theoretical difficulties. If as Linnaeus thought, species were fixed, there would be no problem, but evolutionary processes cause species to change continually, and to grade into one another. A species is often defined as the largest group of organisms in which two individuals can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, when looked at more closely it is problematic. For example, with hybridization, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Among organisms that reproduce only asexually, the concept of a reproductive species breaks down, and each clone is potentially a microspecies. Problems also arise when dealing with fossils, since reproduction cannot be examined. Other ways of defining species include their karyotype, DNA sequence, morphology, behavior or ecological niche.
All species are given a two-part name, a “binomial” (see below). The first part of a binomial is the genus to which the species belongs. The second part is called the specific name or the specific epithet (in botanical nomenclature, also sometimes in zoological nomenclature). For example, Boa constrictor is one of four species of the Boa genus.
Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time. Charles Darwin’s 1859 book The Origin of Species explained how species could arise by natural selection. That understanding was greatly extended in the 20th century through genetics and population ecology. Genetic variability arises from mutations and recombination, while organisms themselves are mobile, leading to geographical isolation and genetic drift with varying selection pressures. Genes can sometimes be exchanged between species by horizontal gene transfer; new species can arise rapidly through hybridization and polyploidy; and species may become extinct for a variety of reasons. Viruses are a special case, driven by a balance of mutation and selection, and can be treated as quasispecies.
As a practical matter, species concepts may be used to define species that are then used to measure biodiversity, though whether this is a good measure is disputed, as other measures are possible.
The commonly used names for kinds of organisms are often ambiguous: “cat” could mean the domestic cat, Felis catus, or the cat family, Felidae. Another problem with common names is that they often vary from place to place, so that puma, cougar, catamount, panther, painter and mountain lion all mean Puma concolor in various parts of America, while “panther” may also mean the jaguar (Panthera onca) of Latin America or the leopard (Panthera pardus) of Africa and Asia. In contrast, the scientific names of species are chosen to be unique and universal; they are in two parts used together: the genus as in Puma, and the specific epithet as in concolor. A species is given a taxonomic name when a type specimen is described formally, in a publication that assigns it a unique scientific name. The description typically provides means for identifying the new species, differentiating it from other previously described and related or confusable species and provides a validly published name (in botany) or an available name (in zoology) when the paper is accepted for publication. The type material is usually held in a permanent repository, often the research collection of a major museum or university, that allows independent verification and the means to compare specimens. Describers of new species are asked to choose names that, in the words of the International Code of Zoological Nomenclature, are “appropriate, compact, euphonious, memorable, and do not cause offence.”
Biologists and taxonomists have made many attempts to define species, beginning from morphology and moving towards genetics. Early taxonomists such as Linnaeus had no option but to describe what they saw: this was later formalized as the typological or morphological species concept. Mayr emphasized reproductive isolation, but this, like other species concepts, is hard or even impossible to test. Many of the concepts are quite similar or overlap, so they are not easy to count.
The evolutionary process by which biological populations evolve to become distinct or reproductively isolated as species is called speciation. Charles Darwin described the role of natural selection in speciation in his 1859 book The Origin of Species. Speciation depends on a measure of reproductive isolation, a reduced gene flow. This occurs most easily in allopatric speciation, where populations are separated geographically and can diverge gradually as mutations accumulate. Reproductive isolation is threatened by hybridization, but this can be selected against once a pair of populations have incompatible alleles of the same gene, as described in the Bateson–Dobzhansky–Muller model. A different mechanism, phyletic speciation, involves one lineage gradually changing over time into a new and distinct form, without increasing the number of resultant species.
A species is extinct when the last individual of that species dies, but it may be functionally extinct well before that moment. It is estimated that over 99 percent of all species that ever lived on Earth, some five billion species, are now extinct. Some of these were in mass extinctions such as those at the ends of the Permian, Triassic and Cretaceous periods. Mass extinctions had a variety of causes including volcanic activity, climate change, and changes in oceanic and atmospheric chemistry, and they in turn had major effects on Earth’s ecology, atmosphere, land surface, and waters. Another form of extinction is through the assimilation of one species by another through hybridization.
Evolution is change in the heritable characteristics of biological populations over successive generations. Evolutionary processes give rise to biodiversity at every level of biological organization, including the levels of species, individual organisms, and molecules.
Repeated formation of new species (speciation), change within species (anagenesis), and loss of species (extinction) throughout the evolutionary history of life on Earth are demonstrated by shared sets of morphological and biochemical traits, including shared DNA sequences. These shared traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct a biological “tree of life” based on evolutionary relationships (phylogenetics), using both existing species and fossils. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, to fossilized multicellular organisms. Existing patterns of biodiversity have been shaped both by speciation and by extinction.
Charles Darwin developed his theory of “natural selection” from 1838 onwards and was writing up his “big book” on the subject when Alfred Russel Wallace sent him a version of virtually the same theory in 1858. Their separate papers were presented together at an 1858 meeting of the Linnaean Society of London. At the end of 1859, Darwin’s book “On the Origin of Species” explained natural selection in detail and in a way, that led to an increasingly wide acceptance of Darwin’s concepts of evolution at the expense of alternative theories.
According to Ernst Mayr, Darwin’s theory actually consists of a number of different theories that can be best understood when they are clearly distinguished from each other. Mayr distinguished five independent theories:
- The non-constancy of species (the basic theory of evolution)
- The descent of all organisms from common ancestors (branching evolution)
- The gradualness of evolution (no saltations, no discontinuities)
- The multiplication of species (the origin of diversity)
- Natural selection
The first and second theories were widely accepted by biologists rather quickly following Darwin’s publication. The other three theories were not widely accepted until the arrival of the so-called modern synthesis in the 20th century (see below).
Evolution by natural selection is a process demonstrated by the observation that more offspring are produced than can possibly survive, along with three facts about populations: 1) traits vary among individuals with respect to morphology, physiology, and behavior (phenotypic variation), 2) different traits confer different rates of survival and reproduction (differential fitness), and 3) traits can be passed from generation to generation (heritability of fitness). Thus, in successive generations members of a population are replaced by progeny of parents better adapted to survive and reproduce in the biophysical environment in which natural selection takes place.
The four most widely recognized evolutionary processes are natural selection (including sexual selection), genetic drift, mutation and gene migration due to genetic admixture. Natural selection and genetic drift sort variation; mutation and gene migration create variation.
The mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis. In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel’s laws of inheritance eventually supplanted most of Darwin’s pangenesis theory. August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin’s pangenesis theory to Weismann’s germ/soma cell distinction and proposed that Darwin’s pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cells structure. de Vries was also one of the researchers who made Mendel’s work well-known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline. de Vries developed a mutation theory to explain how new variants originate. This led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries. In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin’s theory, genetic mutations, and Mendelian inheritance was thus reconciled.
In the 1920s and 1930s the so-called modern synthesis connected natural selection and population genetics, based on Mendelian inheritance, into a unified theory that applied generally to any branch of biology. The modern synthesis explained patterns observed across species in populations, through fossil transitions in paleontology, and complex cellular mechanisms in developmental biology. The publication of the structure of DNA by James Watson and Francis Crick in 1953 demonstrated a physical mechanism for inheritance. Molecular biology improved our understanding of the relationship between genotype and phenotype. Advancements were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees. In 1973, evolutionary biologist Theodosius Dobzhansky penned that “nothing in biology makes sense except in the light of evolution,” because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.
All life on Earth shares a common ancestor known as the last universal common ancestor (LUCA), which lived approximately 3.5–3.8 billion years ago.
In terms of practical application, an understanding of evolution has been instrumental to developments in numerous scientific and industrial fields, including agriculture, human and veterinary medicine, and the life sciences in general. Discoveries in evolutionary biology have made a significant impact not just in the traditional branches of biology but also in other academic disciplines, including biological anthropology, and evolutionary psychology.
In biology, a phylum (plural: phyla) is a level of classification or taxonomic rank below Kingdom and above Class. Traditionally, in botany the term division has been used instead of phylum. Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 33 phyla, the plant kingdom Plantae contains about 14, and the fungus kingdom Fungi contains about 8 phyla. Current research in phylogenetics (see below) is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta.
The term phylum was coined by Ernst Haeckel from the Greek phylon, “race, stock,” related to phyle, “tribe, clan.” In plant taxonomy, August W. Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi.
Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan. At its most basic, a phylum can be defined in two ways: as a group of organisms with a certain degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition).
In biology, phylogenetics (Greek: phylé, phylon = tribe, clan, race + genetikós = origin, source, birth) is the study of the evolutionary history and relationships among individuals or groups of organisms (e.g. species, or populations). These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny (also known as a phylogenetic tree) – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the “end”, or the present, in an evolutionary lineage. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.
Taxonomy is the identification, naming and classification of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline. The degree to which taxonomies depend on phylogenies (or classification depends on evolutionary development) differs depending on the school of taxonomy: phenetics (Greek: phainein - to appear) ignores phylogeny altogether and attempts to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them.
Taxonomy (from Ancient Greek taxis, meaning ‘arrangement’, and nomia, meaning ‘method’) is the science of defining and naming groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus and species. The Swedish botanist Carl Linnaeus (1707–1778) is regarded as the father of taxonomy, as he developed a system known as Linnaean taxonomy for categorization of organisms and binomial nomenclature for naming organisms.
With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct.
Linnaeus ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species, which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. He not only introduced the standard of class, order, genus, and species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower. Thus, the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century. Currently, plant and animal taxonomists regard Linnaeus’ work as the “starting point” for valid names (at 1753 and 1758 respectively). Names published before these dates are referred to as “pre-Linnaean”, and not considered valid (with the exception of spiders published in Svenska Spindlar). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.
Whereas Linnaeus classified for ease of identification, the idea of the Linnaean taxonomy as translating into a sort of dendrogram of the Animal- and Plant Kingdoms was formulated toward the end of the 18th century, well before On the Origin of Species was published. Among early works exploring the idea of a transmutation of species were Erasmus Darwin’s 1796 Zoönomia and Jean-Baptiste Lamarck’s Philosophie Zoologique of 1809. The idea was popularized in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.
With Darwin’s theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. Tree of life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds. Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842. The resulting description, that of dinosaurs “giving rise to” or being “the ancestors of” birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, paleontologists worked to understand the history of animals through the ages by linking together known groups. With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place.
The cladistic method has emerged since the 1960s. In 1958, Julian Huxley used the term clade. Later, in 1960, Cain and Harrison introduced the term cladistic. The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks. A taxon is called monophyletic, if it includes all the descendants of an ancestral form. Groups that have descendant groups removed from them (e.g. dinosaurs, with birds as offspring group) are termed paraphyletic, while groups representing more than one branch from the tree of life are called polyphyletic. The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades. Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.
Well before Linnaeus, plants and animals were considered separate Kingdoms. Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five and six-kingdom systems being the most common.
Domains are a relatively new grouping. First proposed in 1977, Carl Woese’s three-domain system was not generally accepted until later. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera), with the Eukaryota for all organisms whose cells contain a nucleus.
Biological classification is a critical component of the taxonomic process. As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species
The “definition” of a taxon is encapsulated by its description or its diagnosis or by both combined. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules. In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code). In the fields of botany, phycology, and mycology, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN).
The initial description of a taxon involves five main requirements:
- The taxon must be given a name based on the 26 letters of the Latin alphabet (a binomial for new species, or uninomial for other ranks).
- The name must be unique (i.e. not a homonym).
- The description must be based on at least one name-bearing type specimen.
- It should include statements about appropriate attributes either to describe (define) the taxon or to differentiate it from other taxa (the diagnosis, ICZN Code, Article 13.1.1, ICN, Article 38). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name.
- These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.
However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies: depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data.
An “authority” may be placed after a scientific name. The authority is the name of the scientist or scientists who first validly published the name. For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as “Elephas maximus Linnaeus, 1758”. The names of authors are frequently abbreviated: the abbreviation L., for Linnaeus, is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities differs slightly between botany and zoology. However, it is standard that if a species’ name or placement has been changed since the original description, the original authority’s name is placed in parentheses.
Cladistics (from Greek klados, i.e., “branch”) is an approach to biological classification in which organisms are categorized based on shared derived characteristics that can be traced to a group’s most recent common ancestor and are not present in more distant ancestors. Therefore, members of a group are assumed to share a common history and are considered to be closely related.
The original methods used in cladistic analysis and the school of taxonomy derived from the work of the German entomologist Willi Hennig, who referred to it as phylogenetic systematics (also the title of his 1966 book); the terms “cladistics” and “clade” were popularized by other researchers. Cladistics in the original sense refers to a particular set of methods used in phylogenetic analysis, although it is now sometimes used to refer to the whole field.
The following terms, coined by Hennig, are used to identify shared or distinct character states among groups of organisms:
A plesiomorphy (“close form”) or ancestral state is a character state that a taxon has retained from its ancestors. When two or more taxa that are not nested within each other share a plesiomorphy, it is a symplesiomorphy (from syn-, “together”). Symplesiomorphies do not mean that the taxa that exhibit that character state are necessarily closely related. For example, Reptilia is traditionally characterized by (among other things) being cold-blooded (i.e., not maintaining a constant high body temperature), whereas birds are warm-blooded. Since cold-bloodedness is a plesiomorphy, inherited from the common ancestor of traditional reptiles and birds, and thus a symplesiomorphy of turtles, snakes and crocodiles (among others), it does not mean that turtles, snakes and crocodiles form a clade that excludes the birds.
An apomorphy (“separate form”) or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature. Features that are derived in individual taxa (a single species or a group that is represented by a single terminal in a given phylogenetic analysis) are called autapomorphies (from auto-, “self”). Autapomorphies express nothing about relationships among groups; clades are identified (or defined) by synapomorphies (from syn-, “together”). For example, the possession of digits that are homologous with those of Homo sapiens is a synapomorphy within the vertebrates. The tetrapods can be singled out as consisting of the first vertebrate with such digits homologous to those of Homo sapiens together with all descendants of this vertebrate (an apomorphy-based phylogenetic definition). Importantly, snakes and other tetrapods that do not have digits are nonetheless tetrapods: other characters, such as amniotic eggs and diapsid skulls, indicate that they descended from ancestors that possessed digits which are homologous with ours.
A character state is homoplastic or “an instance of homoplasy” if it is shared by two or more organisms but is absent from their common ancestor or from a later ancestor in the lineage leading to one of the organisms. It is therefore inferred to have evolved by convergence or reversal. Both mammals and birds are able to maintain a high constant body temperature (i.e., they are warm-blooded). However, the accepted cladogram explaining their significant features indicates that their common ancestor is in a group lacking this character state, so the state must have evolved independently in the two clades. Warm-bloodedness is separately a synapomorphy of mammals (or a larger clade) and of birds (or a larger clade), but it is not a synapomorphy of any group including both these clades. Hennig’s Auxiliary Principle states that shared character states should be considered evidence of grouping unless they are contradicted by the weight of other evidence; thus, homoplasy of some feature among members of a group may only be inferred after a phylogenetic hypothesis for that group has been established.
The terms plesiomorphy and apomorphy are relative; their application depends on the position of a group within a tree. For example, when trying to decide whether the tetrapods form a clade, an important question is whether having four limbs is a synapomorphy of the earliest taxa to be included within Tetrapoda: did all the earliest members of the Tetrapoda inherit four limbs from a common ancestor, whereas all other vertebrates did not, or at least not homologously? By contrast, for a group within the tetrapods, such as birds, having four limbs is a plesiomorphy. Using these two terms allows a greater precision in the discussion of homology, in particular allowing clear expression of the hierarchical relationships among different homologous features.
It can be difficult to decide whether a character state is in fact the same and thus can be classified as a synapomorphy, which may identify a monophyletic group, or whether it only appears to be the same and is thus a homoplasy, which cannot identify such a group. There is a danger of circular reasoning: assumptions about the shape of a phylogenetic tree are used to justify decisions about character states, which are then used as evidence for the shape of the tree. Phylogenetics uses various forms of parsimony to decide such questions; the conclusions reached often depend on the dataset and the methods. Such is the nature of empirical science, and for this reason, most cladists refer to their cladograms as hypotheses of relationship. Cladograms that are supported by a large number and variety of different kinds of characters are viewed as more robust than those based on more limited evidence.
A monophyletic group is a group of organisms that forms a clade, which consists of all the descendants of a common ancestor. Monophyletic groups are typically characterized by shared derived characteristics (synapomorphies), which distinguish organisms in the clade from other organisms. The arrangement of the members of a monophyletic group is called a monophyly.
A group is paraphyletic if it consists of the group’s last common ancestor and all descendants of that ancestor excluding a few—typically only one or two—monophyletic subgroups. The group is said to be paraphyletic with respect to the excluded subgroups. The arrangement of the members of a paraphyletic group is called a paraphyly.
A polyphyletic (Greek for “of many races”) group is a set of organisms, or other evolving elements, that have been grouped together but do not share an immediate common ancestor. The term is often applied to groups that share characteristics that appear to be similar but have not been inherited from common ancestors; these characteristics are known as homoplasies, and the development and phenomenon of homoplasies is known as convergent evolution. The arrangement of the members of a polyphyletic group is called a polyphyly.
A.11 Animal Clades
A.12 Non-bilaterian animals
Several animal phyla are recognized for their lack of bilateral symmetry, and are thought to have diverged from other animals early in evolution. Among these, the sponges (Porifera) were long thought to have diverged first, representing the oldest animal phylum. They lack the complex organization found in most other phyla. Their cells are differentiated, but in most cases not organized into distinct tissues. Sponges typically feed by drawing in water through pores. However, a series of phylogenomic studies from 2008–2015 have found support for Ctenophora, or comb jellies, as the basal lineage of animals. This result has been controversial, since it would imply that sponges may not be so primitive, but may instead be secondarily simplified. Other researchers have argued that the placement of Ctenophora as the earliest-diverging animal phylum is a statistical anomaly caused by the high rate of evolution in ctenophore genomes.
The Ctenophora and the sponges are unique among the animals in lacking true hox genes. The presence of a Hox/Parahox gene in the Placozoa suggests that either the Porifera or the Ctenophora are the most basal animal clades.
Hox genes (a subset of homeotic genes) are a group of related genes that control the body plan of an embryo along the head-tail axis. In evolutionary developmental biology, homeotic genes are genes which regulate the development of anatomical structures in organisms. After the embryonic segments have formed, the Hox proteins determine the type of appendages (e.g. legs, antennae, and wings in fruit flies) or the different types of vertebrae (in humans) that will form on a segment. Hox proteins thus confer segmental identity, but do not form the actual segments themselves. Mutations in the Hox genes can result in body parts and limbs in the wrong place along the body. The protein product of each Hox gene is a transcription factor. Each Hox gene contains a well-conserved DNA sequence known as the homeobox. Hox genes are thus a subset of the homeobox transcription factor genes. In many animals, the organization of the Hox genes in the chromosome is the same as the order of their expression along the anterior-posterior axis of the developing animal, and are thus said to display co-linearity.
Among the other phyla, the Ctenophora and the Cnidaria, which includes sea anemones, corals, and jellyfish, are radially symmetric and have digestive chambers with a single opening, which serves as both the mouth and the anus. Both have distinct tissues, but they are not organized into organs. There are only two main germ layers, the ectoderm and endoderm, with only scattered cells between them. As such, these animals are sometimes called diploblastic. The tiny placozoans are similar, but they do not have a permanent digestive chamber.
The Myxozoa, microscopic parasites that were originally considered Protozoa, are now believed to have evolved within Cnidaria.
A.13 Bilaterian animals
The remaining animals form a monophyletic group called the Bilateria. For the most part, they are bilaterally symmetric, and often have a specialized head with feeding and sensory organs. The body is triploblastic, i.e. all three germ layers are well-developed, and tissues form distinct organs. The digestive chamber has two openings, a mouth and an anus, and there is also an internal body cavity called a coelom or pseudocoelom. There are exceptions to each of these characteristics, however—for instance adult echinoderms are radially symmetric, and certain parasitic worms have extremely simplified body structures.
Genetic studies have considerably changed our understanding of the relationships within the Bilateria. Most appear to belong to two major lineages: the deuterostomes and the protostomes, the latter of which includes the Ecdysozoa, and Lophotrochozoa. The Chaetognatha or arrow worms have been traditionally classified as deuterostomes, though recent molecular studies have identified this group as a basal protostome lineage.
In addition, there are a few small groups of bilaterians with relatively cryptic morphology whose relationships with other animals are not well-established. For example, recent molecular studies have identified Acoelomorpha and Xenoturbella as forming a monophyletic group, but studies disagree as to whether this group evolved from within deuterostomes, or whether it represents the sister group to all other bilaterian animals (Nephrozoa). Other groups of uncertain affinity include the Rhombozoa (also known as Dicyemida) and Orthonectida. One phyla, the Monoblastozoa, was described by a scientist in 1892, but so far there have been no evidence of its existence.
A.14 Deuterostomes and protostomes
Deuterostomes differ from protostomes in several ways. Animals from both groups possess a complete digestive tract. However, in protostomes, the first opening of the gut to appear in embryological development (the archenteron) develops into the mouth, with the anus forming secondarily. In deuterostomes the anus forms first, with the mouth developing secondarily. In most protostomes, cells simply fill in the interior of the gastrula to form the mesoderm, called schizocoelous development, but in deuterostomes, it forms through invagination of the endoderm, called enterocoelic pouching. Deuterostome embryos undergo radial cleavage during cell division, while protostomes undergo spiral cleavage.
All this suggests the deuterostomes and protostomes are separate, monophyletic lineages. The main phyla of deuterostomes are the Echinodermata and Chordata. The former are radially symmetric and exclusively marine, such as starfish, sea urchins, and sea cucumbers. The latter are dominated by the vertebrates, animals with backbones. These include fish, amphibians, reptiles, birds, and mammals.
In addition to these, the deuterostomes also include the Hemichordata, or acorn worms, which are thought to be closely related to Echinodermata forming a group known as Ambulacraria. Although they are not especially prominent today, the important fossil graptolites may belong to this group.
The Ecdysozoa are protostomes, named after the common trait of growth by moulting or ecdysis. The largest animal phylum belongs here, the Arthropoda, including insects, spiders, crabs, and their kin. All these organisms have a body divided into repeating segments, typically with paired appendages. Two smaller phyla, the Onychophora and Tardigrada, are close relatives of the arthropods and share these traits. The ecdysozoans also include the Nematoda or roundworms, perhaps the second largest animal phylum. Roundworms are typically microscopic, and occur in nearly every environment where there is water. A number are important parasites. Smaller phyla related to them are the Nematomorpha or horsehair worms, and the Kinorhyncha, Priapulida, and Loricifera. These groups have a reduced coelom, called a pseudocoelom.
The Lophotrochozoa, evolved within Protostomia, include two of the most successful animal phyla, the Mollusca and Annelida. The former, which is the second-largest animal phylum by number of described species, includes animals such as snails, clams, and squids, and the latter comprises the segmented worms, such as earthworms and leeches. These two groups have long been considered close relatives because of the common presence of trochophore larvae, but the annelids were considered closer to the arthropods because they are both segmented. Now, this is generally considered convergent evolution, owing to many morphological and genetic differences between the two phyla. Lophotrochozoa also includes the Nemertea or ribbon worms, the Sipuncula, and several phyla that have a ring of ciliated tentacles around the mouth, called a lophophore. These were traditionally grouped together as the lophophorates. but it now appears that the lophophorate group may be paraphyletic, with some closer to the nemerteans and some to the molluscs and annelids. They include the Brachiopoda or lamp shells, which are prominent in the fossil record, the Entoprocta, the Phoronida, and possibly the Bryozoa or moss animals.
The Platyzoa include the phylum Platyhelminthes, the flatworms. These were originally considered some of the most primitive Bilateria, but it now appears they developed from more complex ancestors. A number of parasites are included in this group, such as the flukes and tapeworms. Flatworms are acoelomates, lacking a body cavity, as are their closest relatives, the microscopic Gastrotricha. The other platyzoan phyla are mostly microscopic and pseudocoelomate. The most prominent are the Rotifera or rotifers, which are common in aqueous environments. They also include the Acanthocephala or spiny-headed worms, the Gnathostomulida, Micrognathozoa, and possibly the Cycliophora. These groups share the presence of complex jaws, from which they are called the Gnathifera.
A.18 Binomial nomenclature
Binomial nomenclature, also called binominal nomenclature or binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just “binomial”), a binomen, binominal name or a scientific name; more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs; the second part - the specific name or specific epithet - identifies the species within the genus. For example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of this system of naming species is credited to Carl Linnaeus, effectively beginning with his work Species Plantarum in 1753. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici (English, Illustrated exposition of plants) many names of genera that were later adopted by Linnaeus.
The application of binomial nomenclature is now governed by various internationally agreed codes of rules, of which the two most important are the International Code of Zoological Nomenclature (ICZN) for animals and the International Code of Nomenclature for algae, fungi, and plants (ICN). Although the general principles underlying binomial nomenclature are common to these two codes, there are some differences, both in the terminology they use and in their precise rules.
In modern usage, the first letter of the first part of the name, the genus, is always capitalized in writing, while that of the second part is not, even when derived from a proper noun such as the name of a person or place. Similarly, both parts are italicized when a binomial name occurs in normal text (or underlined in handwriting). Thus the binomial name of the annual phlox (named after botanist Thomas Drummond) is now written as Phlox drummondii. When handwritten, a binomial name should be underlined.
In scientific works, the “authority” for a binomial name is usually given, at least when it is first mentioned, and the date of publication may be specified.
A.19 The Geologic Time Scale
The geologic time scale (GTS) is a system of chronological dating that relates geological strata (stratigraphy) to time. It is used by geologists, paleontologists, and other Earth scientists to describe the timing and relationships of events that have occurred during Earth’s history. The tables of geologic time spans, presented here, agree with the nomenclature, dates and standard color codes set forth by the International Commission on Stratigraphy (ICS).
The primary defined divisions of time are eons, in sequence the Hadean, the Archean, the Proterozoic and the Phanerozoic. The first three of these can be referred to collectively as the Precambrian supereon. Eons are divided into eras, which are in turn divided into periods, epochs and ages.
Studies of strata, the layering of rocks and earth, gave naturalists an appreciation that Earth may have been through many changes during its existence. These layers often contained fossilized remains of unknown creatures, leading some to interpret a progression of organisms from layer to layer.
Nicolas Steno in the 17th century was one of the first naturalists to appreciate the connection between fossil remains and strata. His observations led him to formulate important stratigraphic concepts (i.e., the “law of superposition” and the “principle of original horizontality”). In the 1790s, William Smith hypothesized that if two layers of rock at widely differing locations contained similar fossils, then it was very plausible that the layers were the same age. William Smith’s nephew and student, John Phillips, later calculated by such means that Earth was about 96 million years old.
In the mid-18th century, the naturalist Mikhail Lomonosov suggested that Earth had been created separately from, and several hundred thousand years before, the rest of the universe. Lomonosov’s ideas were mostly speculative. In 1779 the Comte du Buffon tried to obtain a value for the age of Earth using an experiment: He created a small globe that resembled Earth in composition and then measured its rate of cooling. This led him to estimate that Earth was about 75,000 years old.
Other naturalists used these hypotheses to construct a history of Earth, though their timelines were inexact as they did not know how long it took to lay down stratigraphic layers. In 1830, geologist Charles Lyell, developing ideas found in James Hutton’s works, popularized the concept that the features of Earth were in perpetual change, eroding and reforming continuously, and the rate of this change was roughly constant. This was a challenge to the traditional view, which saw the history of Earth as static, with changes brought about by intermittent catastrophes. Many naturalists were influenced by Lyell to become “uniformitarians” who believed that changes were constant and uniform.
Early work on developing the geologic time scale was dominated by British geologists, and the names of the geologic periods reflect that dominance. The “Cambrian”, (the classical name for Wales) and the “Ordovician”, and “Silurian”, named after ancient Welsh tribes, were periods defined using stratigraphic sequences from Wales. The “Devonian” was named for the English county of Devon, and the name “Carboniferous” was an adaptation of “the Coal Measures”, the old British geologists’ term for the same set of strata. The “Permian” was named after Perm, Russia, because it was defined using strata in that region by Scottish geologist Roderick Murchison. However, some periods were defined by geologists from other countries. The “Triassic” was named in 1834 by a German geologist Friedrich Von Alberti from the three distinct layers (Latin trias meaning triad)—red beds, capped by chalk, followed by black shales—that are found throughout Germany and Northwest Europe, called the ‘Trias’. The “Jurassic” was named by a French geologist Alexandre Brongniart for the extensive marine limestone exposures of the Jura Mountains. The “Cretaceous” (from Latin creta meaning ‘chalk’) as a separate period was first defined by Belgian geologist Jean d’Omalius d’Halloy in 1822, using strata in the Paris basin and named for the extensive beds of chalk (calcium carbonate deposited by the shells of marine invertebrates) found in Western Europe.
British geologists were also responsible for the grouping of periods into eras and the subdivision of the Tertiary and Quaternary periods into epochs. In 1841 John Phillips published the first global geologic time scale based on the types of fossils found in each era. Phillips’ scale helped standardize the use of terms like Paleozoic (“old life”) which he extended to cover a larger period than it had in previous usage, and Mesozoic (“middle life”) which he invented.
When geologists first recognized that rock strata represented successive time periods, time scales could be estimated only very imprecisely since estimates of rates of change were uncertain. While creationists had been proposing dates of around six or seven thousand years for the age of Earth based on the Bible, early geologists were suggesting millions of years for geologic periods, and some were even suggesting a virtually infinite age for Earth. Geologists and paleontologists constructed the geologic table based on the relative positions of different strata and fossils, and estimated the time scales based on studying rates of various kinds of weathering, erosion, sedimentation, and lithification. Until the discovery of radioactivity in 1896 and the development of its geological applications through radiometric dating during the first half of the 20th century, the ages of various rock strata and the age of Earth were the subject of considerable debate.
The first geologic time scale that included absolute dates was published in 1913 by the British geologist Arthur Holmes. He greatly furthered the newly created discipline of geochronology and published the world-renowned book The Age of the Earth in which he estimated Earth’s age to be at least 1.6 billion years.
Today, we know that the age of the Earth is approximately 4.54 ± 0.05 billion years. This dating is based on evidence from radiometric age-dating of meteorite material and is consistent with the radiometric ages of the oldest-known terrestrial and lunar samples.
By their chemical nature, rock minerals contain certain elements and not others; but in rocks containing radioactive isotopes, the process of radioactive decay generates exotic elements over time. By measuring the concentration of the stable end product of the decay, coupled with knowledge of the half-life and initial concentration of the decaying element, the age of the rock can be calculated. Typical radioactive end products are argon from decay of potassium-40, and lead from decay of uranium and thorium. If the rock becomes molten, as happens in Earth’s mantle, such nonradioactive end products typically escape or are redistributed. Thus the age of the oldest terrestrial rock gives a minimum for the age of Earth, assuming that no rock has been intact for longer than the Earth itself.
Following the development of radiometric age-dating in the early 20th century, measurements of lead in uranium-rich minerals showed that some were in excess of a billion years old. The oldest such minerals analyzed to date—small crystals of zircon from the Jack Hills of Western Australia—are at least 4.404 billion years old. Calcium–aluminum-rich inclusions—the oldest known solid constituents within meteorites that are formed within the Solar System—are 4.567 billion years old, giving a lower limit for the age of the solar system.
It is hypothesized that the accretion of Earth began soon after the formation of the calcium-aluminum-rich inclusions and the meteorites. Because the exact amount of time this accretion process took is not yet known, and the predictions from different accretion models range from a few million up to about 100 million years, the exact age of Earth is difficult to determine. It is also difficult to determine the exact age of the oldest rocks on Earth, exposed at the surface, as they are aggregates of minerals of possibly different ages.
A.20 Plant anatomy
Plant anatomy is the study of the structure of plant cells and tissues, whereas plant morphology is the study of their external form. All plants are multicellular eukaryotes, their DNA stored in nuclei. The characteristic features of plant cells that distinguish them from those of animals and fungi include a primary cell wall composed of the polysaccharides cellulose, hemicellulose and pectin, larger vacuoles than in animal cells and the presence of plastids with unique photosynthetic and biosynthetic functions as in the chloroplasts. Other plastids contain storage products such as starch (amyloplasts) or lipids (elaioplasts).
The bodies of vascular plants including clubmosses, ferns and seed plants (gymnosperms and angiosperms) generally have aerial and subterranean subsystems. The shoots consist of stems bearing green photosynthesizing leaves and reproductive structures. The underground vascularized roots bear root hairs at their tips and generally lack chlorophyll. Non-vascular plants, the liverworts, hornworts and mosses do not produce ground-penetrating vascular roots and most of the plant participates in photosynthesis. The sporophyte generation is nonphotosynthetic in liverworts but may be able to contribute part of its energy needs by photosynthesis in mosses and hornworts.
The root system and the shoot system are interdependent – the usually nonphotosynthetic root system depends on the shoot system for food, and the usually photosynthetic shoot system depends on water and minerals from the root system. Cells in each system are capable of creating cells of the other and producing adventitious shoots or roots. Stolons and tubers are examples of shoots that can grow roots. Roots that spread out close to the surface, such as those of willows, can produce shoots and ultimately new plants. In the event that one of the systems is lost, the other can often regrow it. In fact it is possible to grow an entire plant from a single leaf, as is the case with Saintpaulia, or even a single cell – which can dedifferentiate into a callus (a mass of unspecialized cells) that can grow into a new plant. In vascular plants, the xylem and phloem are the conductive tissues that transport resources between shoots and roots. Roots are often adapted to store food such as sugars or starch, as in sugar beets and carrots.
Stems mainly provide support to the leaves and reproductive structures, but can store water in succulent plants such as cacti, food as in potato tubers, or reproduce vegetatively as in the stolons of strawberry plants or in the process of layering. Leaves gather sunlight and carry out photosynthesis. Large, flat, flexible, green leaves are called foliage leaves. Gymnosperms, such as conifers, cycads, Ginkgo, and gnetophytes are seed-producing plants with open seeds. Angiosperms are seed-producing plants that produce flowers and have enclosed seeds. Woody plants, such as azaleas and oaks, undergo a secondary growth phase resulting in two additional types of tissues: wood (secondary xylem) and bark (secondary phloem and cork). All gymnosperms and many angiosperms are woody plants. Some plants reproduce sexually, some asexually, and some via both means.
A.21 Plant tissues
In plant anatomy, tissues are categorized broadly into three tissue systems:
- Epidermis - Cells forming the outer surface of the leaves and of the young plant body.
- Vascular tissue - The primary components of vascular tissue are the xylem and phloem. These transport fluid and nutrients internally.
- Ground tissue - Ground tissue is less differentiated than other tissues. Ground tissue manufactures nutrients by photosynthesis and stores reserve nutrients.
Plant tissues can also be divided differently into two types:
- Meristematic tissue consists of actively dividing cells, and leads to increase in length and thickness of the plant. The primary growth of a plant occurs only in certain, specific regions, such as in the tips of stems or roots. It is in these regions that meristematic tissue is present.
- Permanent tissue is formed when cells from meristematic tissues that take up a specific role lose the ability to divide. This process of taking up a permanent shape, size and a function is called cellular differentiation. Cells of meristematic tissue differentiate to form different types of permanent tissue.
There are 3 types of permanent tissues:
- Parenchyma (para - ‘beside’; chyma - ‘in filling, loose, unpacked’) is the bulk of a substance. In plants, it consists of relatively unspecialised living cells with thin cell walls that are usually loosely packed so that intercellular spaces are found between cells of this tissue. This tissue provides support to plants and also stores food. In some situations, a parenchyma contains chlorophyll and performs photosynthesis, in which case it is called a chlorenchyma. In aquatic plants, large air cavities are present in parenchyma to give support to them to float on water. Such a parenchyma type is called aerenchyma.
- Collenchyma is Greek word where “Collen” means gum and “chyma” means infusion. It is a living tissue of primary body like Parenchyma. Cells are thin-walled but possess thickening of cellulose, water and pectin substances (pectocellulose) at the corners where number of cells join together. This tissue gives a tensile strength to the plant and the cells are compactly arranged and have very little inter-cellular spaces. It occurs chiefly in hypodermis of stems and leaves. It is absent in monocots and in roots. Collenchymatous tissue acts as a supporting tissue in stems of young plants. It provides mechanical support, elasticity, and tensile strength to the plant body. It helps in manufacturing sugar and storing it as starch. It is present in the margin of leaves and resist tearing effect of the wind.
- Sclerenchyma is Greek word where “Sclrenes” means hard and “chyma” means infusion. This tissue consists of thick-walled, dead cells. These cells have hard and extremely thick secondary walls due to uniform distribution of lignin. Lignin deposition is so thick that the cell walls become strong, rigid and impermeable to water.
The coelom is the main body cavity in most animals and is positioned inside the body to surround and contain the digestive tract and other organs. The word coelom comes from Greek: koîlos hollow, cavity. Coelom formation begins in the gastrula stage. The developing digestive tube of an embryo forms as a blind pouch called the archenteron.
In Protostomes, the coelom forms by a process known as schizocoely. The archenteron initially forms, and the mesoderm splits into two layers: the first attaches to the body wall or ectoderm, forming the parietal layer and the second surrounds the endoderm or alimentary canal forming the visceral layer. The space between the parietal layer and the visceral layer is known as the coelom or body cavity. Examples of protostome coelomates include earthworms, snails, clams, slugs and octopuses.
In Deuterostomes, the coelom forms by enterocoely: mesoderm buds from the walls of the archenteron and hollows to become the coelomic cavities. Some examples of deuterostome coelomates are sea urchins, fish, sea stars and humans.
A coelom can absorb shock or provide a hydrostatic skeleton. It can also support an immune system in the form of coelomocytes that may either be attached to the wall of the coelom or may float about in it freely. The fluid inside the coelom is known as coelomic fluid. The coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste.
In the past, some zoologists grouped bilaterian animal phyla based on characteristics related to the coelom for practical purposes, knowing, and explicitly stating, that these groups were not phylogenetically related. Animals were classified in three informal groups according to the type of body cavity they possess, in a non-taxonomic, utilitarian way, as the Acoelomata, Pseudocoelomata, and Coelomata. These groups were never intended to represent related animals, or a sequence of evolutionary traits.
However, this scheme was followed by a number of college textbooks and some general classifications, but is now almost totally abandoned as a formal classification.
Coelomate animals or Coelomata (also known as eucoelomates — “true coelom”) have a body cavity called a coelom with a complete lining called peritoneum derived from mesoderm (one of the three primary tissue layers). The complete mesoderm lining allows organs to be attached to each other so that they can be suspended in a particular order while still being able to move freely within the cavity. Most bilateral animals, including all the vertebrates, are coelomates.
Pseudocoelomate animals have a pseudocoelom (literally “false cavity”), which is a fluid filled body cavity. Tissue derived from mesoderm partly lines the fluid filled body cavity of these animals. Thus, although organs are held in place loosely, they are not as well organized as in a coelomate. All pseudocoelomates are protostomes; however, not all protostomes are pseudocoelomates. An example of a Pseudocoelomate is the roundworm. Pseudocoelomate animals are also referred to as Hemocoel and Blastocoelomate.
Acoelomate animals, like flatworms, have no body cavity at all. Semi-solid mesodermal tissues between the gut and body wall hold their organs in place.