Animal Taxonomy, Phylogeny, And Organization
7AnimalTaxonomy,Phylogeny, andOrganizationThis Hawaiian spiny lobster (Panulirus marginatus) is a member of one of the950,000 extant animal species that zoologists have named in a manner thatcreates order out oftbe Ir mendous diversity of animal forms.Chapter Outline7.1 Taxonomy and PhylogenyA Taxonomic HierarchyNomenclatureMolecular Approaches to AnimalSystematicsDomains and KingdomsAnimal Systematics7.2 Patterns of OrganizationSymmetryOther Patterns of Organization7.3 Higher Animal TaxonomyBiologists have identified approximately 1.6 million species, more than three-fourthsof which are animals. Many zoologists spend their lives grouping animals accordingto shared characteristics. These groupings reflect the order found in living systemsthat is a natural consequence of shared evolutionary histories. Often, the work ofthese zoologists involves describing new species and placing them into their properrelationships with other species. Obviously, much work remains in discovering andclassifying the world's 4 to 10 million undescribed species.Rarely do zoologists describe new taxa above the species level (see figure 1. 4).In 1995, however, R. M. Kirstensen and P. Funch of the University of Copenhagendescribed a new animal species-Symbian pandora-on the mouthparts of Notwaylobsters (Nephrops norvegicus). This species is so different that it has been assignedto a new phylum-the broadest level of animal classification (figure 7.1). Thedescription of this new phylum, Cycliophora, is a remarkable event that brings thetotal number of recognized extant animal phyla to 36. These same researchers alsodescribed a new group of animals (Micrognathozoa) from springs in Greenlandin 2000. Both of these groups of animals are discussed in chapter 10. Taxonomistshave discovered that these two new groups of animals are related to each other,and to other animals, in specific ways. This chapter describes the principles usedby zoologists to investigate, and describe, relationships between groups of animals.7 .1TAXONOMY AND PHYLOGENYLEARNING OUTCOMES1. Justify the statement that "taxonomy reflects phylogeny."2. Explain why the goal of phylogenetic systematics is to arrange animals intomonophyletic groups.One of the characteristics of modern humans is our ability to communicate with aspoken language. Language not only allows us to communicate but also helps usencode and classify concepts, objects, and organisms that we encounter. To makesense out of life's diversity, we need more than just names for organisms. A potpourriof more than a million animal names is of little use to anyone. To be useful, a namingsystem must reflect the order and relationships that arise from evolutiona1y processes.The study of the kinds and diversity of organisms and of the evolutionary relation ships among them is called systematics (Gr. systema, system ikos, body of facts)or taxonomy (Gr. taxis, arrangement L. nominalis, belonging to a name). Thesestudies result in the description of new species and the organization of animals intogroups (taxa) based on degree of evolutionary relatedness. The work of taxonomists
Animal Taxonomy, Phylogeny, and OrganizationFIGURE 7.1The Most Recently Described Phylum, Cydiophora. Systematistsgroup animals according to evolutionaiy relationships. Usually, thework of systematists results in newly described species (or speciesfor which new information has been uncovered) being placed inhigher taxonomic categories along with previously studied species.They rarely describe new higher taxonomic groups because findingan organism so different from any previously known organism isunlikely. Svmbion pandora (shown here) was discovered in 1995and was distinctive enough for the description of an entirely newphylum, Cycliophora. The individuals shown here are covering themouthparts of a lobster and are about 0.3 mm long. Since 1995,additional Symbian species have been described from lobsters otherthan Nephrops noruegicus.113species (table 7.1). As one moves down through the hierarchyfrom domain toward species, one is looking at groups derivedfrom more recent ancestors and a smaller subset of more closelyrelated animals (seeji'gure 1.4). Taxonomists have the option ofsubdividing these ranks (e.g., subphylum, superclass, and infra- class) to express relationships between any two ranks.Even though the work of von Linne predated modemevolutiona1y the01y, many of his groupings reflect evolution- my relationships. Morphological similarities between two ani mals have a genetic basis and are the result of a commonevolutiona1y hist01y. Thus, in grouping animals according toshared characteristics, von Linne often grouped them accord ing to their evolutionaiy relationships.The Linnaean taxonomic hierarchy has limitations formodem biology. Above the species level, the definitions ofwhat constitutes a paiticular taxon are not precise. For exam ple, there is no definition of what constitutes a family. The catfamily, Felidae, has 36 species and the ground beetle family,Carabidae, has more than 40,000 species. There are no criteriato establish that these two families represent the same level ofdivergence from a common ancestor or that the time frame fordivergence in the two groups is related in any meaningful way.As we will see later in this chapter, recently derivedcharacteristics are more important than are ancestral charac teristics in establishing evolutiona1y relationships. Traditionalclassification systems were established without distinguishingbetween recently derived and ancestral characteristics. Theconsequence of these limitations is that many older taxonomichierarchies are not useful in making evolutionary predictions,and errors in older interpretations are being revealed.Nomenclatureresults in a phylogeny for a group of animals. A phylogeny(Gr. phylon, race geneia, origin) is a description of the evolu- tiona1y histo1y of a group of organisms and is usually depictedusing tree diagrams that will be introduced in this chapter.A Taxonomic HierarchyModem taxonomy is rooted in the work of Karl von Linne(Carolus Linnaeus) (1707-1778). His binomial system (seechapter 1) is still used today. Von Linne also recognized that dif ferent species could be grouped into broader categories basedon shared characteristics. Any grouping of animals that sharesa particular set of characteristics forms an assemblage called ataxon (pl., taxa). For example, a housefly (Musca domestica),although obviously unique, shares certain characteristics withother flies (the most impoitant of these being a single pair ofwings). Based on these similarities, all true flies form a logical,more inclusive taxon. Fmther, all true flies share certain charac teristics with bees, butterflies, and beetles. Thus, these animalsform an even more inclusive taxon. They are all insects.All animals are given names associated with eight taxo nomic ranks arranged hierarchically (from broad to specific):domain, kingdom, phylum, class, order, family, genus, andDo you call certain freshwater crustaceans crawdads, cray fish, or crawfish? Do you call a common sparrow an Englishsparrow, a barn sparrow, or a house sparrow? The binomialsystem of nomenclature brings order to a chaotic world ofcommon names. Common names have two problems. First,they va1y from count1y to country, and from region to region . r. ·: - f,. TAXONOMIC CATEGORIES OF A HUMAN AND A DOGTAXONHUMANDOMESTIC eHomoHomo iclaeCanisCanis /upis
114CHAPTER SEVENwithin a country. Some species have literally hundreds of lifferenl common names. Biology transcends regional andnationalistic boundaries, and so must the names of whatbiologists study. Second, many common names refer to taxo nomic categories higher than the species level. Most differentkinds of pillbugs (class Crustacea, order Isopoda) or mostdifferent kinds of crayfish (class Crustacea, order Decapoda)cannot be distinguished from a superficial examination. Acommon name, even if you recognize it, often does notspecify a particular species.Nomenclature (L. nominalis, belonging to a name calator, to call) is the assignment of a distinctive name toeach species. The binomial system of nomenclature is univer sal and clearly indicates the level of classification involvedin any description. No two kinds of animals have the samebinomial name, and every animal has only one correct name,as required by the International Code of Zoological Nomen clature, thereby avoiding the confusion that common namescause. The genus of an animal begins with a capital letter,the species epithet begins with a lowercase letter, and theentire scientific name is italicized or underlined because it isderived from Latin or is latinized. Thus, the scientific name ofhumans is written Homo sapiens. When the genus is under stood, the binomial name can be abbreviated H. sapiens.Molecular Approachesto Animal SystematicsIn recent years, molecular biological techniques have providedimpottant information for taxonomic studies. The relatednessof animals is reflected in the gene products (proteins) ani mals produce and in the genes themselves (the sequence ofnitrogenous bases in DNA). Related animals have DNA derivedfrom a common ancestor. Genes and proteins of related ani wab, Ll1e1efu1e, a1e mo1e si111ilai tha11 ge11es and pioteins fromdistantly related animals. Sequencing the nuclear DNA andthe mitochondrial DNA of animals has become commonplace.Mitochondrial DNA is useful in taxonomic studies because mito chondria have their own genetic systems and are inheritedcytoplasmically. That is, mitochondria are transmitted fromparent to offspring through the egg cytoplasm and can be usedto trace maternal lineages. As you will see in the next section,the sequencing of ribosomal RNA has been used extensively instudying taxonomic relationships.Although molecular techniques have proven to beextremely valuable to animal taxonomists, they will notreplace traditional taxonomic methods. Molecular and tradi tional methods of investigation will probably always be usedto complement each other in taxonomic studies.Domains and KingdomsThe highest levels of classification in the taxonomic hierarchyare domains and kingdoms. Classification, like all areas of sci ence, is based on the support of hypotheses that best explainsets of obse1Yations, and our knowledge of evolutionary rela tionships is tentative and always open to revision when newevidence surfaces. Nowhere is this characteristic of sciencemore apparent than in the history of higher taxonomy.In recent years, studies of ribosomal RNA (rRNA) haveprovided a wealth of data that have been used to study theevolution of the earliest life-forms. Ribosomal RNA is excel lent for studying the evolution of early life on eatth. It is anancient molecule, and it is present and retains its function invittually all organisms. In addition, rRNA changes very slowly.Recall that ribosomal RNA makes up a po1tion of ribosomes the organelle responsible for the translation of messenger RNAinto protein. This slowness of change, called evolutionaryconservation, indicates that the protein-producing machineryof a cell can tolerate little change and still retain its vital func tion. Evolutionary conservation of this molecule means thatclosely related organisms (recently diverged from a commonancestor) are likely to have similar ribosomal RNAs. Distantlyrelated organisms are expected to have ribosomal RNAs that areless similar, but the differences are small enough that the rela tionships to some ancestral molecule are still apparent.Molecular systematists compare the base sequences inribosomal RNA of different organisms to find the number ofpositions in the RNAs where bases are different. They enterthese data into computer programs and examine all possiblerelationships among the different organisms. The system atists then decide which arrangement of the organisms bestexplains the data.Studies of ribosomal RNA have led systematists to theconclusions that all life shares a common ancestor and thatthere are three major evolutiona1y lineages (figure 7.2). TheEubacteria is the domain containing the bacteria. Theseorganisms are the most abundant organisms, with more than70 phylum-level lineages. Seven of these lineages have spe cies that are human pathogens. The root of the rRNA tree hastwo branches; one of these branches leads to the Eubacteria.The second branch of the rRNA tree is shared by Archaea andEukarya. The Archaea is a domain containing microbes thatare distinct from bacteria in genetic structure and function.They are more similar to the Euka1ya in regard to the structureof chromatin and regulation of gene function. The Archaeahave a cell wall structure that is different from the bacteria.These differences unite a diverse group of microbes. Someof the most notable for us are those that live in extremeenvironments. Some of these "extremeophiles" are able tolive in high-temperature environments (up to 121 C). Others liveat ve1y cold temperatures within glacial ice. Still others live inocean depths at pressures 600-1,000 times atmospheric pres sure. The Eukarya is the domain containing organisms withcompa1tmentalized cells. Compartmentalization permits theevolution of specialization within cells. In the Euka1ya, thenuclear membrane separates transcription and translationevents. Mitochondrial and chloroplast membranes compart mentalize energy processing. True multicellularity and theevolution of tissues, organs, and organ systems evolved onlyin this lineage.
Animal Taxonomy, Phylogeny, and OrganizationDomain Eubacterla115Domain Are;:haeaUte's commort originFIGURE 7.2Three Lineages of Life. Ribosomal RNA sequencing suggests that the three domains of life can be traced to a common ancestry between3.5 and 2.5 billion years ago. Horizontal gene transfer (dashed lines) was prevalent in the primitive cells that gave rise to these three lineages.The base of the tree of life is thus net-like. HGT continues today but is less common. Within the Eukarya, there are probably six lineagesof protists and three groups that are traditionally considered kingdoms. Members of each of these kingdoms are theoretically traceable to asingle ancestor. These kingdoms are the Animalia, Fungi, and Plantae. The Cryptomycota is a group of fungus-like organisms that are eithervery different from other fungi or make up an entirely new branch of the Eukarya tree.Taxonomies are traditionally built assuming that genesare passed between generations in a species lineage, a pro cess called vertical gene transfer. Recent studies have foundevidence that genes have moved between species, a processcalled horizontal gene transfer (HGT). HGT results in spe cies that are in different lineages sharing genes. HGT wasprevalent in the early history of life, probably because bound aries between cells and species were less fixed than they arenow. As a result of HGT, evolutionary biologists view the baseof the tree of life as a web or net rather than a set of two orthree distinct lineages. The current view is that all life origi nated from a set of primitive cells that evolved togetherbetween 3.5 and 2.5 billion years ago. These primitive cellshad relatively few genes that were freely swapped throughHGT. Eventually, the three domains of life emerged fromthese earliest cells (see figure 7.2). The kingdom level of clas sification is used to refer to groups within each domain thatcan be traced to a single common ancestor. Three kingdomswithin Eukarya are usually considered valid, single-ancestorlineages: Plantae (the plants), Fungi (the fungi), and Animalia(the animals). In 2011, a new branch of the Eukarya tree wasdescribed. The Cryptomycota is a group of freshwater organismsvery closely related to the fungi. Whether or not they repre sent a group of very different fungi or an entirely new branchof Eukarya is yet to be determined. Another set of six lineages,called supergroups, includes all single-celled eukaryans (e.g.,Amoeba, Paramecium, and Volvox). This set of lineages wasformerly designated as a single kingdom "Protista." This king dom designation has been discarded and should not be usedin this formal sense because it represents multiple lineages.Four of the six protist supergroups contain animal-like organ isms and are discussed in chapter 8. The inclusion of animal like protists (protozoa) in general zoology courses is part of atradition that originated with older taxonomic systems. These1·1x mo111ic .'iystems inducl id animal-like·mnAnimationJ rolii-ilS 'I.' :.1 phylum (Protozoa) within theThrno Domainsanim.:iJ kingdom.Animal SystematicsThe goal of animal systematics is to arrange animals into groupsthat reflect evolutionary relationships. Ideally, these groupsshould include the most recent ancestral species and all of itsdescendants. Such a group is called a monophyletic group
116CHAPTER SEVEN(figure 7.3). Polyphyletic groups do not contain the mostrecent common ancestor of all members of the group. Mem bers of a polyphyletic group have at least two phylogeneticorigins. Since it is impossible for a group to have more thanone most recent ancestor, a polyphyletic group reflects insuffi cient knowledge of the group. A paraphyletic group includessome, but not all, descendants of a most recent common ances tor. Paraphyletic groups may also result when knowledge ofthe group is insufficient and the relationships need clarificationin genetic and evolutiona1y contexts (see.figure 7.3).In making decisions regarding how to group animals,taxonomists look for attributes called characters that indi cate relatedness. A character is virtually anything that hasa genetic basis and can be measured-from an anatomicalfeature to a sequence of nitrogenous bases in DNA or RNA.Two kinds of characters are recognized by taxonomists.Homologous characters (see chapter 4) are characters that arerelated through common descent. Vertebrate legs and wingsof birds are homologous characters. Analogous characters areresemblances that result from animals adapting under simi lar evolutiona1y pressures. The latter process is sometimescalled convergent evolution. Homoplasy is a term appliedto analogous resemblances. The similarity between the wingsof birds and insects is a homoplasy. Homologies are usefulin classifying animals, homoplasies are not. The presence ofone or more homologous characters in two animals indicatessome degree of relatedness between the animals. They had acommon ancestor at some point in their evolutionary history.As in any human endeavor, different approaches tosolving problems are preferred by different groups of people.That is also the case with animal systematics. Two popularPolyphyletic Grouprv1onophyletic GioupFIGURE 7.3Evolutionary Groups. An assemblage of species 1-8 isa polyphyletic group because species 1-6 have a differentancestor than species 7 and 8. An assemblage of species 3-6 isa paraphyletic group because species 1 and 2 share the sameancestor as 3-6, but they have been left out of the group. Anassemblage of species 1-6 is a monophyletic group because itincludes all of the descendants of a single ancestor.approaches to animal systematics include evolutiona1y sys tematics and phylogenetic systematics (cladistics).Phylogenetic Systematics or CladisticsPhylogenetic systematics (cladistics) is one approach toanimal systematics. The goal of cladistics is the generation ofhypotheses of genealogical relationships among monophyleticgroups of organisms. Cladists believe that homologies of recentorigin are most useful in phylogenetic studies. Attributes ofspecies that are old and have been retained from a com mon ancestor are referred to as ancestral character states orplesiomorphies (Gr. pleiso, near morphe, form). In cladisticstudies, these ancestral character states are common to all mem bers of a
Taxonomy, Phylogeny, and Organization Chapter Outline 7.1 Taxonomy and Phylogeny A Taxonomic Hierarchy Nomenclature Molecular Approaches to Animal Systematics Domains and Kingdoms Animal Systematics 7.2 Patterns of Organization Symmetry Other Patterns of
R.Br. and few small genera (5). The taxonomy and phylogeny of Astragalus are very challenging. In the present paper we will review the background of taxonomic and phylogenetic studies on Astragalus, the sources of complexity in the taxonomy and phylogeny of the genus, and future pe
Ant phylogeny Although impressionistic tree-like diagrams can be found in earlier literature (e.g., Wheeler 1920, Emery 1920, Morley 1938), a useful starting point for discussing modern work on ant phylogeny is Brown’s (1954) paper on the internal phylogeny and subfamily classification
molecular biology, taxonomy, phylogeny and speciation. The Triticeae have been placed together with Brachypodieae (Hack.) Hayek and Bromeae Dum, in the monophyletic subgroup Triticeae Macfarlane and Watson of the Pooideae A. Brown5,6 characterized by having endosperm with simple and rounde
Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the volutionary histories of multiple genes Maiko Watanabe1*, Takahiro Yonezawa2, Ken-ichi Lee3, Susumu Kumagai3, Yoshiko Sugita-Konishi1, Keiichi Goto4 and Yukiko Hara-Kudo1 BMC Evolutionary
Taxonomy and Molecular Phylogeny of Usnea rubicunda and U. rubrotincta (Parmeliaceae, Lichenized Ascomycotina) Yoshihito OHMURA Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba, Ibaraki, 305-0005 JAPAN ＊E-ma
Molecular Taxonomy and Phylogeny 121 Whilst rRNA genes may provide optimal lev-els of variation for investigating Meloidogyne phy-logeny, they are not without significant theoretical and analytical drawbacks. The single biggest obs-tacle in using rRNA genes is that, unlike p
Molecular phylogeny and taxonomy of the genus Veloporphyrellus Yan-Chun Li Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China Beatriz Ortiz-Santana US Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot .Cited by: 21Publish Year: 2014Author: Yan-Chun Li, Beatriz Ortiz-Santana, Nian
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