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Phylogenetic systematics, especially involving molecular data, has had a remarkable impact on systematic biology. Numerous tree-building computer programs exist for the reconstruction of phylogenies, and many packages are available for analysis of population genetic data for estimating genetic divergence within and among populations. These advances have come about through the joining of statistical algorithms, computer programs, and DNA base-pair sequence and fragment data. Deeper genomic data are on the horizon for use with similar questions, and the next several years will witness many spectacular genetic advances. While great progress is being made on analytical approaches with molecular data in systematics, the use of the results of these analyses in biological classification has solidified into a dogmatic view, which has impeded further progress. Emphasis still remains on using only synapomorphies, even single characters, for delimitation of groups, on insisting that sister groups should have the same rank, and admitting only holophyletic (= monophyletic s. str.) groups. Evolutionary divergence within lineages and reticulate evolution are often ignored. As a result of these processes, paraphyletic groups, i.e., monophyletic groups that do not contain all descendants from a common ancestor, are often rejected. Evolutionary systematics takes the processes of descent and modification into consideration for reconstructing phylogenetic relationships involving many dimensions. This symposium presents various approaches for recognizing cladogenetic, anagenetic, and reticulate evolution in different organisms, which help reveal micro- and macro-evolutionary processes. Controversy still exists regarding how taxonomists should incorporate the diversity of evolutionary patterns and processes into biological classification. Case studies demonstrate that purely phylogenetic (cladistic) concepts of classification are unsatisfactory in cases of non-hierarchical relationships. Contributions also deal with the controversial question of recognition of paraphyletic groups in classification.
Early evolutionary thinkers proposed relatively simple models to describe processes of evolution, and these are the basis of evolutionary models still used today. Recent research has since shown that evolutionary relationships among plants can be complex and difficult to reconstruct even from molecular data. In plants there is a continuum of processes, ranging from reticulate relationships within a sexually reproducing population, incomplete lineage sorting and hybridization between recently diverged species, allopolyploidy between more distantly related species, to symbioses and endosymbiosis. These aspects of plant biology can create practical problems for interpreting bifurcating gene trees and identifying species. The promise of “omics” is that it will provide data and analyses to improve our understanding of the nature of species and their phylogenetic relationships. We highlight the importance of distinguishing evolutionary processes and evolutionary models, and stress that improving the understanding of micro-evolutionary processes is necessary to inform current debate on whether or not to accept paraphyletic species.
Biological classification aims at establishing ordering systems for organisms. Principles of classification, however, differ in their criteria and in their information content. Cladistic classification emphasizes information on descent, but the strict application of logical inclusiveness leads in practice to disregard of modification and to a lack of information on evolutionarily relevant features. Phenetics provides information on similarity regardless of descent. Evolutionary classification maximizes information on evolution by combining information on descent and modification, but it relaxes the requirement of inclusiveness. In practice, this means accepting holo- and paraphyletic taxa, but rejecting polyphyletic groups. Review of a recently published case study of the species-rich and cosmopolitan genus Ranunculus demonstrates how evolutionary classification can be performed in practice. A hypothesis of descent was reconstructed by phylogenetic analysis of DNA sequence markers plus morphological and karyological characters. Based on this backbone phylogeny, information content on morphology, karyology, and ecology was used as a criterion for delimitation of infrageneric taxa. This concept resulted in the subdivision of a more basal, paraphyletic Ranunculus subg. Auricomus and the holophyletic Ranunculus subg. Ranunculus. On a sectional level, 14 holophyletic and two paraphyletic sections plus one monotypic section were classified. Holophyletic sections mostly reflect extinction gaps, while paraphyletic groups appear in clades that have reticulate evolution and/or ecological shifts. Classification of paraphyletic and monotypic sections preserves information on morphology, ecology, and evolutionary processes. This pluralistic approach is justified as it best reflects the diversity of the genus. The principle of broadening criteria maximizes information on descent and modification. Evolutionary classification facilitates practicability and stability of taxonomic work, as the broadening of criteria restricts the number of equally valid options for classification. For users, preserving information content on phenotypes aids practicability, because the connection to traditional literature and to modern information systems is optimally maintained.
The transfer of Dryandra R. Br. to Banksia L. f. was based on the use of holophyly (monophyly s. str.) as an essential criterion for recognition of taxa. The transfer was significant in scope and focuses on two iconic genera of plants in Western Australia. It has been accepted by some and rejected by others. It is one of many examples in a debate that pits recent genetic analysis against centuries of field and herbarium studies, and cladists against classical taxonomists. I argue that: (1) there are sound morphological characters distinguishing Dryandra from Banksia and they should be maintained as genera; (2) paraphyly should be accepted in biological classification; (3) scientifically, and for a morphologically complex genus of 137 specific and infraspecific taxa, the use of 11 taxa for the molecular analysis of Dryandra was insufficient; (4) some morphological data, mapped onto the cladogram a posteriori, were incorrect; (5) molecular cladistic approaches should complement rather than override pre-existing and extensive classifications based on phenotypic traits; (6) the acceptance of the transfer for the Australian Plant Census was premature according to guidelines published by Australian herbaria.
Genera of flowering plants that are endemic to oceanic islands are often of great biological interest. These groups represent adaptive complexes that confer distinction to the islands or archipelagos in which they are found, and this often results in a focus on their conservation. In recent decades, numerous molecular phylogenetic (and other evolutionary) studies have been done on island genera, hence providing much valuable new information on relationships and evolution of island groups. Genera restricted to oceanic islands derive evolutionarily from parental stocks usually in continental regions. These parental genera are often themselves evolutionarily successful, being particularly adept at dispersal, adaptation, and speciation. These immigrants to isolated oceanic islands derive from common ancestors of large and diverse parents or directly from within the lineages themselves. If in the latter case the island derivatives are treated at the generic level, then the parental genus becomes paraphyletic in a cladistic sense. In this circumstance there are three alternatives to classification of the island group: (1) treat both the island complex as a distinct holophyletic genus and the progenitor as a coordinate, but paraphyletic, genus; (2) submerge the island complex into the parental genus, perhaps at the subgeneric or sectional level, creating a larger holophyletic genus; or (3) divide the parental genus and island complex into a series of smaller genera in such a manner that all become holophyletic. A synthesis of recent investigations on 100 endemic island genera and relatives was completed in the Bonin Islands, Canary Islands, Galápagos Islands, Hawaiian Islands, Madeiran Islands, Robinson Crusoe Islands, and St. Helena. The results show that 64 genera are still accepted and remain uninvestigated or are seen as holophyletic in phylogenetic analyses. Seven have already been submerged based on non-cladistic results, and 29 are viewed as being nested within larger parental genera. Of this latter group, 15 of the genera are still being recognized at this time; six have been recommended as belonging within their parental genera; and eight have been formally transferred into the progenitor genera with combinations made. If further actions were to be taken based on strict holophyly, following the second alternative mentioned above, then these 29 genera would disappear as endemics in their islands or archipelagos. This would result in an overall average drop of 31.9% endemic genera in oceanic islands worldwide (based on the sample analyzed). With the third alternative, new generic concepts for the island and progenitor taxa would need to be worked out. Instead of recognizing genera on the basis of simple holophyly, genera should be based on cohesiveness, distinctness, and monophyly s.l. (i.e., including paraphyly and holophyly). A statistic is provided as a means for making these assessments quantitatively. The importance of unique and/or divergent character change for classification of island lineages is also stressed.
On the basis of multidisciplinary studies on the tribe Rubieae, we contribute to the current discussion on paraphyly and supraspecific taxa that do not contain all descendant species of an ancestral clade. Rubieae belong to the large, predominantly tropical and woody family Rubiaceae and include possibly ≤ 1000 mostly temperate and herbaceous species with worldwide distribution. Our studies span distinctive groups throughout the tribe, consist of a maximum parsimony analysis of plastid atpB-rbcL and rpL32-trnL DNA sequences, and are summarized in a condensed strict consensus tree. A corresponding two-dimensional scheme illustrates alternative hypotheses for phylogenetic relationships among all major Rubieae clades identified. The small relictual genus Kelloggia Torr. in Benth. & Hook. f., formerly excluded from the Rubieae, is supported as a remnant of the ancestors of the tribe. Didymaea Hook. f. and Rubia L. represent early phylogenetic side lines. All other Rubieae form a large monophyletic crown group with the traditional genera Asperula L. being polyphyletic and Galium L. paraphyletic. Changes in the circumscription of these and other genera are thus inevitable. The necessity of accepting paraphyletic taxa as well as the positive and negative aspects of taxonomic splitting versus lumping within Rubieae are discussed. Additionally, lectotypes are designated for one section of Asperula---Asperula sect. Dioicae Airy Shaw & Turrill, typified by A. conferta Hook. f.—and for three sections of Galium---Galium sect. Leiogalium (DC.) Ledeb., typified by G. sylvaticum L.; Galium sect. Lophogalium K. Schum., typified by G. multiflorum Kellogg; and Galium sect. Depauperata Pobed., typified by G. songaricum Schrenk ex Fisch. & C. A. Mey.
The theoretical basis for cladistic classification into monophyletic (holophyletic) ranked taxa is fatally flawed and is promoting bad taxonomy. Biological classification that takes account of evolutionary history may be based on two main factors—lines of descent and extent of divergence represented by morphological and other characters. In taxonomy a balance must be found between lines of descent and characters, and insistence on one at the expense of the other will give unacceptable results. Much confusion has arisen in systematics from the failure to appreciate that taxonomy, which groups organisms into ranked taxa (families, genera, etc.), is essentially different from grouping them into clades. These two processes are based on conflicting hierarchies and have different methodologies and functions. For several decades, however, the cladistics movement has adopted lines of descent rather than characters as the sole basis of taxonomy, insisting that only complete clades should be recognized as taxa. But as soon as one imposes ranks on a phylogeny, one must create paraphyletic taxa. These are natural products of evolution, which should be recognized in taxonomy. When ranks are adopted without acceptance of paraphyletic taxa, taxonomic free fall sets in, and every clade sinks into those taxa to which its original ancestor is referable. The clash of hierarchies results in absurdity, extending to sinking the entire plant kingdom into one family and one genus, but this has been strangely overlooked by the cladistic side. Adoption of ranked taxa is incompatible with recognition of only complete clades. Merely because one taxon falls phylogenetically within the clade of another taxon at the same rank does not necessarily mean that it must be included in it taxonomically. New characters will have arisen during evolution, which should be taken into account. A monophyletic (= holophyletic) system recognizing only complete clades is logically possible only if ranks are abandoned, as in the PhyloCode. It may be referred to as a “cladification” and the process producing it as “cladonomy,” which are quite different concepts from a “classification” and “taxonomy.” In a classification we have a hierarchical series of taxa at different ranks, while in a cladification we merely have a hierarchy of clades nesting within successively bigger clades. Cladistic taxonomy is particularly nonsensical in paleobotany, where our Linnaean taxonomic system and our code of nomenclature apply just as they do for extant plants. Cladograms are not classifications, and they need critical taxonomic assessment. The great majority of users of taxonomy are interested in characters and not cladistic theory. A general purpose classification is needed, requiring acceptance of paraphyletic taxa that are defined by characters as well as lines of descent. Examples in the dicot flowering plant families are given in which cladistic principles have imposed excessive insistence on lines of descent at the expense of evolution of characters, producing what many regard as bad taxonomy.
Investigation of caulistic macroevolution in an evolutionary tree often requires separate support measures for exemplar groups, and for the taxon they represent. A taxon may be actually or cryptically heterophyletic on a molecular tree. Congruence between branch order of morphological and molecular cladograms is not as important as is congruence between inferred macroevolutionary transformations at the taxon level as caulistic elements on an evolutionary tree. Unsampled paraphyletic branches can affect perceived progenitor-descendant relationships and may be inserted in a molecular tree to help explain lack of congruent caulistic inferences without affecting calculated branch order. Integrable and non-integrable analyses must be combined for scientific completeness. Support for inferred macroevolutionary transformations may be estimated from either the amount of present-day paraphyly in densely sampled, related groups or from clade support and nearest neighbor interchange.
Plants are essential for the survival and sustainability of both humans and wildlife species around the world. However, human activities have directly and indirectly affected almost all plants, which in turn have produced cascading effects on humans and wildlife through disruption of crucial ecosystem services and wildlife habitat. Understanding such complex interactions is crucial for developing better policies that reconcile the needs of an ever-growing human population with biodiversity conservation. Using the coupled human and natural systems (CHANS) framework, this article synthesizes research on the complex interactions of plant species, giant pandas, and people. The CHANS framework is particularly useful for uncovering key patterns and processes behind plant-animal interactions modified by human activities. Our synthesis shows that many human factors, including socioeconomic and demographic, together with other factors (e.g., projected global climate change), exhibit reciprocal interactions with pandas and the plant species that comprise their habitat. Although substantial efforts have been made to preserve plants and wildlife, much work still remains to be done, including the expansion and more effective management of protected areas, use of native plant species in reforestation/afforestation programs, and active participation of local residents in conservation actions.