Tree
of Life Peer Review: Notes for ReviewersTree
of Life Peer Review: Notes for ReviewersThis page provides guidance to people who have agreed to serve as reviewers for Tree of Life (ToL) pages. The ToL review process shares many characteristics of the traditional peer-review system familiar to all scientists, but the design and content of the ToL project are quite different from printed academic communications. Reviewers will therefore benefit from a brief introduction to the general structure of the project and to our expectations of the content of a ToL page.
Each ToL page should provide a general treatment of an entire group of organisms; it should include a balanced treatment of alternative hypotheses about relationships; it should provide interesting information on all notable aspects of the organisms. The audience of a page includes both the educated layman and systematists. Pages for well-known, commonly encountered organisms will be more often visited by the non-biologists, and these trunk pages must be written with them in mind. For these pages, at least the Introduction and the start of the Characteristics section should be intelligible to the educated layman, but the remainder can be more jargon-rich. (This recommendation is less relevant to obscure groups, as those pages will be less visited by non-biologists.)
For further information, see the following sections:
More information can be found at the Tree's home page or by emailing us at treegrow@ag.arizonal.edu.
The ToL project consists of various explanatory pages at the home site, as well as three classes of pages authored by contributors: the branch pages and leaf pages, which together form the main body of the Tree, and accessory or lichen pages, which are additional pages that are attached to the Tree's branches and leaves.
Branch pages are all of the Tree pages that have (or will eventually have) other ToL pages descended from them. Each of these pages shows a phylogeny or classification of subgroups, and the Discussion of Phylogenetic Relationships is an important featured text section. Leaf pages are the ToL pages presenting information about individual species. They are the terminal pages on the Tree, and are attached to apical branches. Accessory or lichen pages are pages that are attached to either branch or leaf pages of the Tree, but are not themselves part of the Tree structure. They do not provide the primary information about the groups of organisms (this is provided on the branch or leaf pages), but instead contain additional information, perhaps including more detailed descriptions of structure, additional details about phylogenetic relationships, more pictures, identification keys, etc. While links to many additional pages can be made from a ToL branch or leaf, only those linked pages that are specially designated and included in the Tree of Life's index are considered ToL accessory pages.
Branch pages of the Tree of Life are composed of the following required elements:
In addition, authors can choose to expand their pages, by adding additional text sections and a section about Information on the Internet.
Each ToL branch page should contain at least one picture of a representative member or members of the clade that is covered on the page. Title illustrations should give the reader a general impression of what the organisms in a given clade look like; they should generally show whole organisms (or substantial portions), not just certain body parts, and good pictures of live specimens are preferred whenever they are available. For some organisms, especially extinct groups, this will not be possible.
Note that the frames around the title figures serve as a link to the 'Title Illustrations' section at the bottom of the page, which contains the captions for the title figures. We have moved the captions for the title figures to the bottom of the page, in order to limit the items that appear on the page above the phylogenetic tree. This tree is the key element of each Tree of Life page and should therefore be as near the top of a page as possible. With the current arrangement, the link from the title figures still provides quick access to the captions, and authors don't have to worry about the amount of text included in the captions.
Each ToL branch page features a phylogenetic tree or, if phylogenetic information is not available, a simple classification of the taxa contained in a group. The tree/classification is the navigational center of a Tree of Life page; it contains a link from the root to the page of the containing group as well as links to the pages of the current group's subgroups.
The tree/classification section of a ToL page should contain all the
taxa included in a given group, i.e., not just the ones that were featured in
a particular phylogenetic analysis, and not just the ones that occur in a particular
faunal region. One reason for this requirement is to emphasize that the phylogenies
presented should not just be the result of a single analysis, but should synthesize
all available information. If the studies on which a page is based used only
exemplar taxa, then authors must add the rest of the known taxa to the tree
or classification on the ToL page. If the phylogenetic relationships within
a certain group of taxa are uncertain, this section of the tree can be displayed
as a polytomy. Taxa of uncertain phylogenetic placement can also be labeled
as incertae sedis (
).
They can either be included in the tree at their putative position, or they
can be listed below the tree.
A Tree of Life page that is complete should contain not only all Recent but
also all extinct (
) members
of a clade. We realize that most pages will currently have to remain incomplete
in this respect. But authors should make an effort to include extinct members
of a clade whenever information on fossil taxa is available.
Taxa that are well established in the taxonomic literature but are suspected
to be non-monophyletic can be included in the tree or classification of a page,
but their questionable status must be clearly indicated. In the classification,
a non-monophyletic label is associated with such taxa, and on the tree, branches
leading to these taxa are characterized by a special format (
).
These symbols can also be used for taxa that are not firmly established as non-monophyletic,
but that are likely so.
Taxa known to be non-monophyletic are actively discouraged from inclusion in the Tree, as they cause great difficulty in the composition and linking of pages.
This section introduces the members of the clade that are represented on the page. The Introduction should explain what kinds of organisms they are, what is unique about them, and in what context the reader might have encountered these organisms before. Authors may talk about the number of species, geographic distribution, relationship to humans, well-known members of the clade, habits of the organisms, habitats, etc. They can also include illustrations of additional members of the clade.
The information contained in the Introduction should apply to the entire clade represented on a page, not just to certain terminal taxa, as discussed in the Characteristics.
This section should not include extensive discussions of any particular topic, and it should be kept relatively brief. If authors want to include more information about a particular topic, we recommend that they place it in a separate section. Furthermore, the Introduction should be easy to read (the target is an educated layman). The Tree of Life project is used in high schools, so we want at least a few sections near the top of the page that can be read by non-biologists.
This section should talk about the general characteristics of the members of a given clade. It might describe some of the unique structural or ecological features of the group, perhaps including a small picture or two. A description of prominent synapomorphies of the clade would be valuable. The start of the Characteristics section should be easy to read (the target is an educated layman), but in later paragraphs it can digress into jargony details for the biologist.
The information contained in the Characteristics section should apply to the entire clade represented on a page, not just to certain terminal taxa. Detailed information about terminal taxa should be contained on the pages for those taxa. The tendency to focus on particular terminal taxa will be especially strong if one of the terminal taxa is much better known than the rest. However, Tree of Life pages should be concerned with all the members of a given clade, and authors should aspire to balance the information given on each page accordingly. In general, the most that should be said about any particular taxon is a brief sentence or two.
There are two reasons for focusing on the entire clade rather than a few terminal taxa. First, separating information to the relevant page will reduce redundancy. But more importantly, overemphasis on certain terminal taxa will obscure the phylogenetic world view presented in the Tree. For example, consider the page for Chordata. The only well-known group within chordates are the vertebrates, and it might seem natural to concentrate on vertebrates on the chordate page. However, this would de-emphasize the unity of the Chordata as a whole and the fascinating connection between such morphologically divergent creatures as sea squirts and birds.
This section should contain a reasonable and fair discussion of alternative hypotheses for the phylogeny of all the subgroups of a given clade. It should not generally discuss the phylogenetic placement of the entire clade; this question is to be addressed on the page of the current clade's containing clade, or in a separate section on the current page.
The Discussion of Phylogenetic Relationships should not go into detailed arguments about evidence, but should concisely summarize the strengths and weaknesses of the various hypotheses (detailed discussion can be provided on an accessory page). Summaries of both morphological and any molecular evidence should be provided. Images of alternative phylogenies should be displayed, if possible. This section should not be simply a list of apomorphies for various nodes; that sort of detail can be presented on a linked page.
The discussion should focus on phylogeny, not classification (although some discussion of past classifications might be necessary here, if those classifications were intended to make claims about phylogeny but were not accompanied by an explicit phylogenetic tree). If authors wish to discuss the nomenclature and classification of the group, that could be done in a separate section.
This section should contain the bibliographic references for the given clade. The references should include not only cited papers, but also other general references about the clade.
Introduction, Characteristics, Discussion of Phylogenetic Relationships, and References sections are required for each completed Tree of Life page. In addition, authors can add additional text sections according to the special requirements of their group. Such additional topics may provide information about biogeography, life history, fossil specimens, topics relating the organisms to humans (e.g. medical importance), etc. If authors want to provide detailed information on any particular topic (i.e., more than three or four paragraphs), we recommend that they create an accessory page for this topic.
In this section, authors should provide a series of links to other internet sites that contain information about the given clade.
Copyright © 1998 David R. Maddison
All rights reserved.