APPENDIX ONE Systematics of Major Parasites Groups

CONTENTS

The science of systematics includes three parts: identification, nomenclature, and classification of living organisms (Grimont 1999).

IDENTIFICATION

Identification is a process whereby an organism is rec­ognized as belonging to a known species within a taxo­nomic hierarchy and designated accordingly (Grimont 1999). The methods of identification vary considerably among taxonomic groups and, where pertinent, are addressed in discussions of these individual groups.

NOMENCLATURE

Biological nomenclature is the system of assigning Latin names to organisms using a universal vocabu­lary. The intention of nomenclature is that each spe­cies in a given taxonomic position should be given a unique name (Grimont 1999). Since the time of Linnaeus, each organism has been given a binomial name; the first is the genus name and is written with the first letter capitalized; the second is the species epithet and normally is not capitalized.

The term species has been defined in a variety of ways. Within evolutionary biology, species typically are identified as natural populations of individuals that are actually or potentially interbreeding, and are isolated reproductively from other such populations (Dobzhansky 1937; Mayr 1942, 1963).

Any biologist may name a new species, provided that the proposal is supported by sufficient data and the appropriate nomenclatural rules for a discipline are fol­lowed. Each group of organisms has specific rules for its proper naming. For example, the International Code OfNomenclature of Bacteria (Sneath 1992) includes rules on how to name bacteria and how to use the names.

CLASSIFICATION SYSTEMS

A classification based on evolutionary relationships is a phylogenetic classification. Cladistics is a method of classification based on evolutionary genealogies alone (Thain and Hickman 2004). While the science of clas­sification generally is designed to reflect evolutionary relationships, these relationships have been very difficult to ascertain for some groups of organisms, including most microorganisms (Bohannon 2008).

Classification of living organisms is a complex field that is continually undergoing significant revi­sions as new techniques and new information arise. R. H. Whittaker broke the historic tradition of a three-kingdom system of classification after recog­nizing that the classification of all organisms as pro­karyotes, animals, or plants was an artificial division that did not reflect their evolutionary relationships (Whittaker 1969). Adding the Kingdoms Fungi and Protista was intended to more closely reflect their presumed evolutionary relationships by attempt­ing to establish monophyletic groups that included an ancestor and all of its descendants, as well as to develop a hierarchical classification to reflect the relationships of these groups (Alexopoulos et al.

Until the early 1990s, the consensus view was that the early descendants of life's last universal com­mon ancestor, a small cell with no distinct nucleus, divided into two prokaryotic (nonnucleated) groups— the bacteria and the archaea (Doolittle 1999, 2000). Later, the archaea were proposed to have given rise to eukaryotic cells, more complex cells with true nuclei that, in turn, gained mitochondria, chloroplasts (among plants), and other organelles by incorpo­rating adaptable bacteria (Doolittle 1999, 2000). Increasingly, evidence emerged that most archaeal and bacterial genomes, and the inferred ancestral eukaryotic nuclear genome, contained genes from multiple sources through the effects of extensive “lateral gene transfer” (Doolittle 1999). Thus it became difficult to propose a clear hierarchical uni­versal classification based on evolutionary relations, because the traditional metaphor of a branching tree no longer appeared to apply (Doolittle 1999).

Instead, it was proposed that a communal, loosely knit community of primitive cells evolved together and developed to a stage where this com­munity broke into several distinct communities that further evolved into three primary domains, or lines of descent: archaea, bacteria, and eukaryotes (Woese 1998). Cells of these early groups each had relatively few genes; while each group was distinct, they also commonly exchanged genes. In time, most gene transfers were thought to have become limited to within each of these three domains (Doolittle 2000).

With further work, there again is a more optimis­tic view about finding a last universal common ances­tor. Following the finding of the large mimivirus in amebae (La Scola et al. 2003), a view emerged that viruses might be the last universal common ancestor (Villarreal 2005).

While numerous classification schemes have been proposed, ranging from two to eight kingdoms (Keeton and Gould 1993), Whittaker's five-kingdom scheme still is most commonly used. For classifica­tion purposes, an initial division typically is made between prokaryotic organisms and eukaryotic organisms. Eukaryotic organisms include organelles such as true nuclei, mitochondria, endoplasmic reticulum, Golgi apparatus, and lysosomes— structures lacking in prokaryotic organisms (Murray et al. 1999). Prokaryotes divide by fission rather than by mitosis or meiosis. Prokaryotes include both the Archaebacteria and Eubacteria (“true bacteria”) (Murray et al. 1999) and are classified in the King­dom Monera (Whittaker 1969). Eukaryotic organ­isms are distributed among the Kingdoms Protista (single-celled eukaryotes), Plantae, Animalia, and Fungi (Whittaker 1969).

A recent revision of single-celled eukaryotic clas­sification based on molecular phylogenies (Adl et al. 2005) incorporates revised thinking about clas­sification. With an emphasis on wildlife diseases, the scheme of Adl et al. (2005) for eukaryotic cells includes the following categories and divisions:

Supergroup Amoebozoa

Entamoebida (parasitic amoeba)

Mastigamoeba (parasitic amoeba)

Supergroup Opisthokonta

Fungi (Parasitic fungi)

Metazoa

Animalia (multicellular animal groups) Platyhelminthes (flatworms) Nematoda (nematodes)

Acanthocephala (spiny-headed worms) Arthropoda (insects, acarina)

Supergroup Rhizaria

Supergroup Archaeplastida

Chloroplastida

Charophyta

Plantae (plants)

Supergroup Chromoalveolata

Alveolata

Apicomplexa (malarias, piroplasms, coccidia) Ciliophora (parasitic ciliates)

Supergroup Excavata

Fornicata (intestinal flagellates)

Parabasilia (intestinal flagellates) Supergroup Euglenozoa (hemoflagellates)

In Adl et al.’s (1995) revision, organisms of former kingdoms such as fungi and animals are proposed as second- and third-level subgroups of one super­group (Opisthokonta); in contrast, many the groups traditionally classified as relatively close have been separated into widely disparate taxonomic groups.

CLASSIFICATION OF PARASITES

Parasites may comprise the majority of species in the world, with parasites outnumbering free-living species four to one according to one estimate (Zimmer 2000). In conventional Darwinian theory, organismal selection often adapts organisms to immediate local environments through specializations that reduce organismal flexibility for future evolution, especially to radically altered conditions (Gould 2002). Parasites may be more extreme examples of this process, with considerable specializations obscuring their evolution­ary affinity to ancestral forms and contemporary free- living forms. Thus, while contemporary perspectives on the classification and taxonomic relations among vari­ous parasite groups will be considered, these perspec­tives often are controversial and continue to change as additional information becomes available. However, in recent years, even microbial classification is becoming more phylogenetically based, and molecular methods are being used to clarify many relationships.

We recognize the progress represented by the recently proposed classification ofeukaryotes (Adl et al. 2005) summarized above, and that scientific under­standing of the basic relationships between organisms continues to change. However, we currently continue work from the more established, traditional five- kingdom system: Monera, Protista, Fungi, Animalia, and Plantae. The only exception is that we will draw on Adl et al. (2005) in discussion of the Kingdom Protista.

With the exception of Plantae, parasites of impor­tance to wildlife are represented in each of Whittaker’s other four kingdoms. Viruses and prions are additional infective agents causing wildlife diseases that gener­ally are not included as living organisms; these are treated as addenda to the five-kingdom system.

In the Kingdom Animalia of Whittaker’s (1969) traditional scheme, several phyla are of importance to wildlife diseases. Members of the Phylum Platyhel- minthes (“flatworms”) all are dorsoventrally flattened.

Members of the Phylum Nematoda are character­ized by bilateral symmetry, and by being round in cross section, elongated, and tapered at both ends. Members of the Phylum Acanthocephala, or “spiny-headed worms,” are a small group of unsegmented parasitic worms characterized by bilateral symmetry (Crompton and Nickol 1985). They are round in cross section, typi­cally with a cylindrical or slightly flattened body and an invertible spiny hold-fast organ at their anterior end.

Members of the Phylum Annelida are bilaterally symmetrical segmented worms with a true coelom. They typically comprise three groups of organisms: Class Polychaeta (sandworms), Class Oligochaeta (earthworms), and Class Hirudinea (leeches) (Mader 1994). Members of the Phylum Arthropoda are bilaterally symmetrical invertebrates with a true hemocoel, chitinous exoskeletons, and jointed legs (“arthro-pods”) (Keeton and Gould 1993).

The Kingdom Protista has several important groups and, for these, we draw on more recent studies reflected in the work of eukaryotic taxonomists (Adl et al. 2005). The major groups addressed are parasitic amebae in the Supergroup Amoebozoa; the malaria parasites, piroplasms, coccidia, and ciliated protozoa in the Supergroup Chromoalveolata; and the flagel­lated protozoa included in the Supergroup Excavata.

Members of the Kingdom Fungi are eukaryotic organisms that lack chlorophyll, roots, leaves, stems, xylem, or phloem; however, they have cell walls with chitin, cellulose, or both. They almost always are non-motile, and reproduce by means of spores (Alexopoulos et al. 1996).

Among prokaryotic organisms, the Kingdom Monera currently contains two significant groups: the Archaebacteria and the Eubacteria. Of these, only the Eubacteria are of importance in the study of wildlife diseases, and further discussion will be focused on them. Eubacteria are single cells or simple associations of simple cells with cellular rather than organismal properties (Holt et al. 1994); occasional filamentous or mycelial forms may occur.

While viruses possess some of the properties of living systems, including having a genome (Villarreal 2004), they are best described as nonliving infec­tious entities rather than living microorganisms (van Regenmortel and Mahy 2004). Interestingly, some viruses can become infected with other viruses, and become “sick” in the process (Ogata and Claverie 2008); this adds a complex element to the debate around the status of virus as living agents. Cur­rent classification schemes for viruses are based on their proposed evolutionary relationships (Buchen- Osmond 2003, van Regenmortel and Mahy 2004).

Recently, infectious proteins (prions), with no nucleic acids (Buchen-Osmond 2003), have been described that are important contributors to some wildlife diseases. Prions (proteinaceous infectious particles 1 “on,” denoting particle) are normal cellu­lar proteins in which some have undergone changes in their folding configuration that, in turn, have led to their becoming pathogenic.

For each major group we provide a general defini­tion of the group, a brief description of some of its distinctive features, and a summary of any recent taxonomic changes.

source: Anderson 2000.

APPENDIX TABLE 3

Platyhelminths (Class Cercomeridia) Important to Wildlife

source: Bush et al. 2001.

sources: Allan 2001, Colwell 2001, Durden 2001, Mullen and Durden 2002.

APPENDIX TABLE 5

Classification for Major Protista Groups Affectingfor Wildlife

APPENDIX TABLE 6

Fungi of Interest in the Study of Wildlife Diseases

(continued)

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