系统发育基本概念

1、Comparative Biology

?Nelson (1970) divided biology into two basic areas. He held that general biology was concerned with investigating biological processes while comparative biology was concerned with investigating biological patterns,and we concur with aspects of this definition. In general biology,the investigator picks organisms that are most likely to be amenable to studying a particular process of interest to them. In comparative biology,the investigator is interested in studying the characteristics of diverse organisms to infer the historical,evolutionary relationships between these organisms. For example,an ethnologist working in the realm of general biology is interested in the mechanistic explanation of a particular stimulus - response reaction.By contrast,the ethnologist working in the realm of comparative biology is interested in how common that stimulus - response reaction might be among organisms and how that stimulus - response reaction has evolved through time. In particular,he or she would be interested in determining if that response to stimulus evolved once or repeatedly. Phylogenetic systematics,like other systematic disciplines,is one comparative approach. The phylogeneticist is interested in estimating the pattern of organic diversity and thus the historical course of evolution. Any and all comparative data are potentially useful in this pursuit,and any and all comparative information can,in theory,be accommodated.

2、Systematics

Systematics is the study of organic diversity as that diversity is relevant to some specified pattern of evolutionary relationship thought to exist among the entities studied. This definition is somewhat narrower than others (e.g.,Mayr,1969 ; Nelson,1970 ),which held systematics synonymous with comparative biology. From our perspective,not all comparative biologists practice systematics,even though all comparative data can be accommodated by systematics. For example,comparative physiologists may not analyze their data phylogenetically,but their data can be incorporated into a phylogenetic analysis or better understood by mapping it onto a well - con? rmed phylogenetic tree.

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3、Taxonomy.

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Taxonomy comprises the theory and practice of describing,naming,? and ordering groups of organisms termed taxa . How the taxa are ordered into classi?cations de? nes the particular approach to taxonomic classi? cation. The? rules for naming are outlined in various Codes of Nomenclature,and these codes are now being challenged in new ways by those who seek to rede?ne taxonomy. This de?nition differs from some authors (e.g.,Simpson,1961 ) who equated taxonomy with systematics.

4、Phylogenetic Systematics

Phylogenetic Systematics. T his is one approach to systematics and taxonomy? that attempts to recover the phylogenetic relationships among taxa and in which formal biological classi?cations are consistent with these relationships. We refer to the discipline as phylogenetics and to those who practice it as phylogeneticists. Another common set of terms is cladistics and cladists . We do not object to these terms (? rst coined by an opponent,1969 ). However,we suggest that it originally implied a preoccupation with branching pattern and a de-emphasis on character evolution,neither of which is true. Indeed,recovering the pattern of character evolution reveals the pattern of branching and speciation. The goal of phylogenetics is to give a complete account of speciation and character evolution.

?5. Taxon.

This is a grouping of organisms at the level associated with the application of proper scienti? c names,or a grouping of such organisms that could be given such a name but is not named as a matter of convention. The plural is taxa. Some taxa (the natural ones) are considered to have an objective reality in nature apart from our ability to ? nd and name them. Taxa in practice are groups named by systematists. As such,they are hypotheses about taxa in nature. As hypotheses,they may be accepted or rejected based on subsequent research,or even on logical grounds. For example,phylogenetic systematists reject paraphyletic taxa on logical grounds because such taxa result in classi?cations that are inconsistent with an accepted phylogenetic tree (Wiley,1981b ). Higher taxa are taxa that include more than one species. Species taxa are the
lowest formally recognized taxa usually considered in phylogenetic analysis.

6、 Monophyletic Group.

A monophyletic group is a taxon comprised of two or more species that includes the ancestral species and all and only the descendants of that ancestral species (Fig. 1.2 a). Monophyletic group is usually considered synonymous with the term clade,and the two terms are frequently
used interchangeably. As used here,species are not monophyletic groups because they are self - referential entities of process while monophyletic groups are neither self-referential nor units of process,except the process of descent. Instead,they are entities of history. Monophyletic groups in nature are real,but again monophyletic groups named by systematists are hypotheses,and these hypotheses stand or fall on the empirical evidence.

?7. Para - and Polyphyletic Groups.

Paraphyletic groups are incomplete groups in which one or more of the descendants of the common ancestor are not included in the group (Fig. 1.2 b). Invertebrata is an example,as are Reptilia (birds and mammals excluded) and Pongidae ( Homo and allied fossil genera excluded). Polyphyletic groups are comprised of descendants of an ancestor not included in the group at all. Homothermia (birds + mammals) would be an example as the ancestor of birds and mammals would presumably be included in Reptilia. Para - and polyphyletic groups are not real in nature. From the phylogenetic perspective,paraphyletic and polyphyletic groups named by systematists are illogical,either through ignorance (group named in the absence of a phylogeny) or practice (as in evolutionary taxonomic practice for naming paraphyletic groups).

8、Sister Group.

In nature,a sister group is a single species or a monophyletic group that is the closest genealogical relative of another single species or
monophyletic group of species (Fig. 1.3 ). True sister groups share a unique common ancestral species — an ancestral species not shared by any other species or monophyletic group. In phylogenetic analysis,a sister group is the hypothesized closest known relative of a group the investigator is analyzing,given current knowledge. Hypotheses of sister group relationship are fundamental to phylogenetic practice. In analyses,the sister group is the most in?uential outgroup for determining the relative merit of presumed homologies to indicate genealogical relationships within the group studied,as outlined in Chapter 6 .

9、Outgroup

An outgroup is a species or higher taxon used in phylogenetic analysis to evaluate which presumed homologs indicate genealogical relationships within the group studied and which are simply primitive characters (Fig.1.3 ). The outgroup is used to root the tree and determine character polarity. The sister group is a special-case outgroup. Critical analysis requires the investigator to consult both the sister group and at least one additional outgroup to make the determination about homologs.

?10、Ingroup

The ingroup is the group that is being analyzed by the investigator. It is shown in Fig. 1.3 as a polytomy because relationships within the group are unresolved before an analysis. Other graphic devices show the ingroup as? a triangle.