Genomically Preserved Plants and Their Nomenclature Author(S): Charles R

Genomically Preserved Plants and Their Nomenclature Author(s): Charles R. Werth and David B. Lellinger Reviewed work(s): Source: Taxon, Vol. 41, No. 3 (Aug., 1992), pp. 513-521 Published by: International Association for Plant Taxonomy (IAPT) Stable URL: http://www.jstor.org/stable/1222823 . Accessed: 06/07/2012 03:16

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http://www.jstor.org AUGUST 1992 513

Genomicallypreserved plants and theirnomenclature

Charles R. Werth1& David B. Lellinger2

Summary Werth, C. R. & Lellinger, D. B.: Genomically preserved plants and their nomenclature. - Taxon 41: 513-521. 1992. - ISSN 0040-0262.

Species that hybridize to form allopolyploids may become extinct, yet may be discovered and characterized through the continued existence and expression of their genomes in their allopolyploid descendants. For purposes of nomenclature, these genomically preserved plants (GPPs) form a third category of plants, along with recent plants and fossils, with which they share certain kinds of characters. GPPs are essential to understanding the phylogeny of some species complexes and can be included as OTUs in phenetic and phylogenetic analyses. A means to provide for the naming, description, and typification of taxa of genomically preserved plants needs to be included in the International code of botanical nomenclature.

Introduction The frequent origin of plant species from interspecific hybrids presents challenges to precepts and procedures in systematics developed principally with diverging lineages in mind. Beyond the obvious taxonomic confusion caused by their morphological intermediacy, special considerations are necessary to integrate hybrids into numerical or phylogenetic analyses (Jensen & Eshbaugh, 1976; Funk, 1985; Wagner, 1983; McDade, 1990) and to treat them nomenclaturally (Wagner, 1969, 1987; Werth & Wagner, 1990). The present paper addresses yet another challenge, one that has begun to emerge from studies of species complexes that include polyploid species of hybrid origin (allopolyploids): the discovery and characterization of previously unknown taxa of antiquity on the basis of their genomic contributions to extant polyploid species. It is the thesis of this paper that species whose genomes are preserved, in whole or in part, by their polyploid derivatives are in many ways equivalent to modern species and fossils presently accommodated by the International code of botanical nomenclature. Necessary amendments of the Code to provide for the description, typification and formal naming of genomically preserved plants (referredto henceforth as GPPs, the singular is GPP) are proposed in a separate paper (Werth& Lellinger, 1992).

Discovery of genomically preservedplants Allopolyploidy, by fixing and stabilizing hybrid genotypes, provides a means by which GPPs can be recognized and described, even long after the plants themselves may have become extinct. Genomes from divergent species are combined to form most allopolyploids, and chromosome pairing is typically restricted (or nearly so) to homologous pairs derived from the same genome. This pairing behavior causes the genotype of the original hybrid to be reconstituted, chromosome for chromosome, gene for gene, in each succeeding generation, as shown by studies of genetic variation

1 Department of Biological Sciences, TexasTech University, Lubbock, TX 79409, U.S.A. 2 Department of Botany MRC-166, Smithsonian Institution, Washington, DC 20560, U.S.A. 514 TAXON VOLUME 41 and inheritance in natural allopolyploids (Bryan & Soltis, 1987; Haufler & al., 1990; Roose & Gottlieb, 1976;Werth & al., 1985a, 1985b). This fixed hybridity thus preserves intact the genetic contribution of each genome; consequently, even after numerous generations the allopolyploid's morphological features remain more or less intermediate between those of its ancestors and its chemical features remain additive. When identification of one or more diploid ancestors of a given allopolyploid has remained unsuccessful in the face of various sources of comparative evidence, investigators have frequently hypothesised that the ancestor(s) may be extinct or at least unknown. As new sources of taxonomic evidence for biosystematic investigation have been developed and refined, it has become possible to infer with increasing certainty that such hypothesised missing taxa existed and to infer with increasing precision character states in which they differ from extant related species. Examples of hypothesised GPPs occur in a number of genera representing diverse taxonomic groups. In angiosperms, for example, the source of the B genome of hexaploid wheat (Triticum aestivum L.) has long been disputed, but is believed to be a species in Triticum sect. Sitopsis (Kimber & Sears, 1987). The diploid species T speltoides Flaksb. was once proposed as the B genome donor (Sarkar & Stebbins, 1956). However,evidence from chromosomal homology (Kimber & Athwal, 1972) and restriction site analysis of repetitive DNAs indicate that "the B genome of T aestivum may have derived from a species that is now extinct and whose closest extant relative may be T speltoides" (Talbert& al., 1991). In ferns, studies of chromosome pairing and/or isozymes have led to hypotheses of missing diploid ancestors for polyploid species of Dryopteris (Wagner, 1971), Cystopteris (Haufler, 1985; Haufler & Windham, 1991), Cryptogramma (Alverson, 1988), and Hemionitis (Ranker & al., 1989). In the case of Hemionitis, a multilocus allozyme genotype was inferred for a missing diploid ancestor of the allotetraploid H. pinnatifida Baker, and its genetic identity with other diploid Hemionitis species was computed (Ranker & al., 1989). Considerable attention has been given to a missing ancestor in Dryopteris. An unknown diploid, informally designated "D. semicristata" was originally hypothesised to account for the observed homology of a genome (designated S) shared by the tetraploids D. carthusiana (Vill.) H. P. Fuchs and D. cristata (L.) A. Gray and the hexaploid D. clintoniana (D. Eaton) Dowell (Wagner, 1971). Evidence from various sources has substantiated the existence of "D. semicristata"and has permitted its character states to be inferred. This evidence includes data on leaf morphology (Werth & Kuhn, 1989; Kuhn & Werth, 1990), trichomes (Viane, 1986), spore morphology (Britton, 1972a, 1972b, 1974), phloroglucinols (Euw & al., 1980, Widen & al., 1975), isozymes (Werth, 1989, 1991), and chloroplast DNA (C. Hutton & D. Stein, pers. comm.). The number of separate observations that support the "D.semicristata" hypothesis is so great that the past or present existence of the species is beyond reasonable doubt. Whether it is truly extinct remains a matter of some discussion, but apparently no known Dryopteris species possesses the appropriate combination of character states. The most likely candidate, D. tokyoensis (Matsum.) C. Chr., was proposed as the missing ancestor on the basis of its phloroglucinol content (Wid6n & Britton, 1985), but has many other character states unlike those of "D. semicristata" (Werth, 1989; Werth & Kuhn, 1989). The emergence of enhanced means for confirming the existence and inferring the character states of GPPs raises questions relevant to their nomenclatural treatment: should they receive formal taxonomic designation and how, in the absence of a AUGUST 1992 515 specimen, should their names be typified? When the possibility of formal status for "Dryopterissemicristata" was first suggested (Werth, 1990), response by systematists was mixed and included suggestions that the nomenclature of such taxa remain informal. However, we are convinced that formal nomenclature is both appropriate and necessary. Our reasoning follows from comparing GPPs as taxonomic entities to those entities presently accommodated by the Code, i.e., modern taxa that are extant (at least historically so) and fossil taxa that are presumably extinct.

Existence in time and space of GPPs Recent species are known from living plants and the specimens made from them, whereas fossil species are known from remains that preserve principally morphological features. Such contrasts are not absolute, for recent species may also be known from the fossil record, and taxa known originally as fossils, such as Metase- quoia (Chaney, 1950), may be discovered alive. Genomically preserved plants, on the other hand, are known from the expression of their genomes in the polyploids to which they are ancestral. To some extent, this evidence is analogous to fossil remains, as discussed in greater detail below. Knowledge of the spatial and temporal range of species varies tremendously. It is fair to say that it is incomplete for all species with respect to the full history of their existence. The distribution of many recent temperate species in human historical time is known in some detail, and extensive information is available on the prehistoric distribution of some recent as well as fossil species. However, the small proportion of any flora that becomes fossilized precludes knowing with certainty that a species was absent at any given time or place in the past. Knowledge of the spatial and temporal occurrence of GPPs is even less certain because the time and place they hybridized cannot be clearly determined. Never- theless, strong inferences may be made from various sources, including present distributional patterns of GPPs' allopolyploid descendants and their extant ancestors. For example, it is likely that the GPP "Dryopterissemicristata" was North American, although the polyploids derived from it have intercontinental distribu- tions, as both extant diploids with which it hybridized to form tetraploids (D. ludovi- ciana (Kunze) Small and D. intermedia (Willd.) A. Gray) are presently North American endemics (Carlson & Wagner, 1982). Fossil occurrences of derived allopolyploids may also help delimit the occurrence of GPPs. Unlike fossils, there is likely to be a limit to the age of a GPP that can be characterized with confidence, for evolution of the polyploid lineage includes events that obscure the evidence of its ancestry (discussed below). Moreover, extinction of ancestral diploids itself will obscure taxonomic understandings that can lead to recognizing genomically preserved taxa. However, it is possible that extensive characterization of nucleotide sequences could allow recognition of relatively ancient GPPs that are obscured with respect to other characters.

Characterstates of GPPs Modern species can be observed as preserved specimens or living organisms that provide a wealth of structural, chemical, ecological, and other characters with various states by which they may be distinguished from and compared to other species (Stuessy, 1990). Species known only as fossils can be characterized to varying degrees for the subset of the foregoing characters that happen to be preserved. This subset is 516 TAXON VOLUME 41 usually limited to morphological, anatomical, and palynological features, although in unusual instances chemical features including secondary compounds (Niklas & Gian- nasi, 1977; Niklas & Gensel, 1977) or even DNA (Soltis & al., 1991)may be studied in favorably preserved fossil remains. Some information on the ecology of fossil species may also be available (Rothwell, 1991). Inevitably, however, fossils remain incompletely characterized compared to their recent counterparts because some characters fail to be preserved (including organs, life cycle stages, chemicals, etc.) or because preservation is imperfect and character states are somewhat altered by fossilization processes (e.g. compression, permineralization, etc.). Similarly to fossils, GPPs may be characterized for a subset of the characters that are available in modern taxa, specifically those that can be observed by the continued existence and expression of the missing taxon's genome. Charactersthat are additive in hybrids are directly observable, provided that one can recognize and subtract the contributions of other genomes that formed the allopolyploid. This may include characters of the karyotype (only chromosomes of "Dryopterissemicristata" pair in the hybrid between D. carthusianaand D. cristata), secondary compounds, allozymes, and DNA sequences or restriction sites. To some degree, non-additive (i.e. averaged) characters, particularly morphological attributes, may be inferred for the GPP by extrapolation from the extant ancestor through the allopolyploid, as has been done for "Dryopterissemicristata" (Werth & Kuhn, 1989; Kuhn & Werth 1990). In some respects, this is analogous to inferring morphological states of a species whose fossil is an impression; the GPPs have left their "impression" on the phenotypic expression of the allopolyploids that are their derivatives. Confidence in the evaluation of all character states will be enhanced if the GPP is ancestral to more than one polyploid, so that congruence of separately inferred character states can be ascertained. Although it is apparent that the preservation of recognizable and characterizable genomes via allopolyploids can endure beyond the extinction of the parental diploid taxon that bore the genome, it is equally clear that evolutionary processes occuring within the polyploid will alter some attributes that the genome possessed as a diploid and eventually will obscure its distinctness. These processes include mutational events such as chromosomal rearrangementsand gene silencing, the latter believed to cause genetic diploidization of ancient polyploids (Gastony, 1991;Haufler, 1987; Picherski & al., 1990), and perhaps occasional intergenomic recombination as well. Mutations may also introduce novel (orphan) alleles and cause chromosomal rearrangements that represent false character states of the GPP that were not present in its ancestor. Experience with isozymes of polyploids suggests, however, that substantially altered genotypes are unlikely to be recognized as GPPs in the first place because gene silencing would likely be more frequent than mutations that produced novel but functional alleles.

Integration of GPPs into phylogenetic analyses The reconstruction of phylogenies is a goal given high priority by many systematists. Although the desirability of incorporating extinct species into a cladistic or phenetic analysis is contentious (Wiley, 1981: 214-221), it is generally agreed that missing taxa may adversely influence perceived relationships in phylogenetic analysis (Gautier & al., 1988). In the case of a reticulately evolved complex, the phylogeny must be con- structed as a reticulogram in which OTUs of hybrid origin are indicated as points on AUGUST 1992 517 converging lines originating from the ancestors (Funk, 1985; Wagner, 1983; Kellog, 1989). It is obvious that a rational reticulogram must include GPPs as divergent OTUs in order to account for those OTUs derived through reticulation. Thus, GPPs are essential elements in understanding and communicating phylogenies. Because numerous character states may be inferred for GPPs, it is feasible to include them as OTUs in phenetic or phylogenetic analyses, especially those based on isozyme or DNA characters (Ranker & al., 1989). Because GPPs are discovered in interspecific hybrids, they will usually be species assignable to the same genus as their allopolyploid descendant. It is possible, however, that the hybrid may be of intergeneric derivation, and that the GPP may be assigned to a different genus from its hybridization partner.

Rationalefor formal nomenclaturefor GPPs Presumably a large number of GPPs await discovery, confirmation, and robust characterization comparable to that of "Dryopteris semicristata". Those presently hypothesised have been named informally, either with a genome designation (e.g., the B genome of wheat, the F genome of Hemionitis pinnatifida), with a provisional epithet (e.g., "D. semicristata" "Cystopterishemifragilis'"), or with a general term such as "hypothetical ancestor". As investigations of polyploid complexes progress, especially with the application of molecular techniques, GPPs will be characterized with increased precision and integrated into phylogenetic hypotheses. As molecular characters acquire increased importance in phylogenetic systematics, GPPs will become fully acknowledged elements of past biodiversity. Moreover, because GPPs can be incorporated into molecular-based phylogenies, their relationship to recent taxa will be more precisely known than will that of most taxa preserved as fossils. It seems inevitable that GPPs will be referredto repeatedly in literaturedealing with systematics, as well as in paleoecological, geological, and conservation literaturethat addresses topics such as extinction episodes. Therefore, the stability of GPP names must be a matter of concern. Inconsistency already exists in the literature as to the designation of the missing Dryopteris ancestor, some authors referring to it as the B genome (Gibby & Walker, 1977; Widen & Britton, 1985), others as the S genome or D. "semicristata"of Wagner (1971). In our opinion, informal nomenclatural status is no more acceptable for GPPs than it would be for fossils.

Validpublication of GPP names Valid publication of GPPs must requiretheir description and typification in a manner parallel to that of modern species or fossils. Descriptions of GPPs will necessarily rely heavily on non-morphological attributes that represent their most certain features. Non-morphological features usually present in species descriptions include principally chromosome numbers, but the inclusion of chemical data will inevitably increase. Often cryptic species are more distinguishable on the basis of chemical features than on morphological ones (Paris & al., 1989). Descriptions of GPPs may include features of the karyotype, secondary chemical compounds, allozymes, restriction site information, and critical nucleotide sequences of specified genome segments, as well as morphological features inferred by extrapolation. Clearly, the attributes of the GPPs most directly observable from their genome, such as nucleotide sequences, are more certain to have been attributes of the 518 TAXON VOLUME 41

GPP than are others, such as extrapolated morphological features that may be distorted by interaction with the other genome(s) in the polyploid and by evolution since the formation of the polyploid. Although GPP descriptions are unorthodox, they would serve their purpose well by providing key diagnostic features useful for discriminating closely related species; see Prop. (148). In addition, data pertaining to the GPP should be clearly differentiated from data pertaining to other genomes (e.g., photographs and other illustrations should be marked). Although characterstates of GPPs may be modified through time, this is not unlike the modification of some character states during the fossilization process or during the preparation of a herbarium specimen. When a GPP has formed more than one polyploid species (as in the case of "Dryopteris semicristata" and "Cystopteris hemifragilis'"),those attributes that are shared by the genome as it is manifested in both polyploids may most confidently be assigned to the GPP and should be emphasized in the description. Descriptions of GPPs must include a statement of the one or more polyploid species believed to possess the genome contributed by the GPP. However,if more than one polyploid species is cited, it is necessary to insure against ambiguity in the application of the name of a GPP resulting from a later taxonomic decision that genomes thought to have been contributed by a GPP to different polyploids are in fact not con- specific. One derived allopolyploid species must be designated as providing the primary evidence for the GPP, and this one must be the species from which the type is derived; see Prop. (149). The greater obstacle to publication of valid names for GPPs is typification, for it is impossible to provide a specimen or an illustration of one to serve as the holotype. It is clear from the present wording of the Code that types of vascular plants should be specimens, whenever possible. Thus, the type of a fossil taxon is the fossil itself and not an interpretivereconstructive illustration. It is equally clear, however,that the purpose of designating a type is to unequivocally affix a name to an entity representing the author's intended usage (Art. 7.2). The Code does in fact provide for typification by means of an illustration in those cases where a specimen cannot be provided (Art. 9.3). In current practice, illustrations are designated as types only in lectotypifications where illustrations or citations of illustrations are part of the protologue. The illustration provision in the Code points the way, we believe, for typification of GPPs without greatly modifying either the letter or spirit of the present Code. The type of a GPP must be an illustration depicting a set of features by which the taxon can be unequivocally distinguished from other species; see Prop. (147). At the present time, isozyme or restriction fragment band patterns and nucleotide sequences appear to be the most robust features, and so should be used. Specifying a nucleotide sequence, in that it depicts the primary structure of a DNA molecule and portrays the genetic information it encodes, is equivalent to an illustration and is to be preferred over a complete chemical diagram of the molecule (cf. Reynolds & Taylor, 1991). Although non-morphological data represent a departure from the specimen (or illustration thereof) that ordinarily serves as the type of a vascular plant, they best provide for unequivocally associating a GPP with its name. In contrast to this, the least certain attributes of a GPP are likely to be its morphological features, for they are inferred by extrapolation, rather than by subtraction. Non-morphological features are routinely used in describing and typifying bacteria, lichens, and some fungi (Hale, 1966), and it has been suggested recently that DNA specimens or sequence "illustrations" could serve as elements of types (Reynolds & Taylor, 1991). AUGUST 1992 519

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