The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.

/pdf/species-concepts-and-species-delimitation-4we3sl6pvr.pdf

Species Concepts and Species Delimitation

Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.

/pdf/a-classification-for-extant-ferns-20xz6lvrz8.pdf

A classification for extant ferns

The Families of the Monocotyledons

Speciation, the process through which new species come into being, is one of the central topics of evolutionary biology. It links the great fields of microand macroevolutionary biology and intersects a wide variety of related biological disciplines, including behavioral biology, ecology, genetics, morphology, paleontology, physiology, reproductive biology, and systematics. For this reason, a persistent controversy regarding the definition of the term species may seem disconcerting. The continual proposal of new species definitions-commonly characterized as alternative species concepts-seems to suggest that there is no general agreement about what species are, and if this is the case, then the possibility of understanding how species come into being also seems unlikely. At the very least, there seems to be considerable potential for misinterpretation and confusion about what different biologists mean when they talk about species and speciation. But the situation is not really as troublesome as it may appear. Although real differences underlie alternative species definitions, there is really less disagreement about species concepts than the existence of so many alternative definitions seems to suggest. Each species definition has a different emphasis, but the various phenomena that they emphasize are all aspects or properties of a single kind of entity. In other words, almost all modem biologists have the same general concept of species. Differences among the many versions of this general concept are at least partly attributable to the complex and temporally extendednature of species and the process or processes through which they come into existence. In many respects, considering speciation as a temporally extended process is the key to understanding the diversity of species definitions. In this chapter, I provide a general theoretical context that accounts for both the unity and the diversity of ideas represented by alternative species definitions. First, I review the major categories of species definitions adopted by contemporary biologists. Next, I present evidence that all modem species definitions describe variants of a single general concept of species. I then discuss how the timeextended nature of species and the diversity of events that occur during the process of speciation provide the basis for the diversity of alternative species definitions. Based on a distinction between species concepts and species criteria, I propose a revised and conceptually unified terminology for the ideas described by contemporary species definitions, and I discuss the significance and limitations of different classes of species definitions. Finally, I examine an interpretation of species criteria that places alternative criteria in direct conflict and thus contains the key to resolving the species problem.

The General Lineage Concept of Species, Species Criteria, and the Process of Speciation

The phylogeny of the subfamilyRubioideae (Rubiaceae) was estimated from sequence variation in therps16 intron (cpDNA) in 143 ingroup and 5 outgroup taxa. The analysis largely confirms a recent one based onrbcL sequences, but branch support is often much stronger. Three of the traditional subfamilies are supported,Rubioideae, Cinchonoideae s. str., andIxoroideae s. l. while there is no support forAntirheoideae. TheRubioideae are the sister group of all otherRubiaceae and comprise the tribesAnthospermeae, Coccocypseleae, Cruckshanksieae, Coussareeae, Gaertnereae, Hedyotideae, Knoxieae, Morindeae, Ophiorrhizeae, Paederieae, Pauridiantheae, Perameae, Psychotrieae, Rubieae, Spermacoceae, Theligoneae, andUrophylleae. TheHamelieae andHillieae belong to theCinchonoideae. Rachicallis andSiemensia should be transferred from theHedyotideae to theCinchonoideae. ThePauridiantheae, Urophylleae, Ophiorrhizeae, andRaritebe form the basalmost subclade of theRubioideae. The second basalmost clade consists of the generaLasianthus andPerama. The third basalmost clade consists of the tribesCoussareeae, Coccocypseleae andCruckshanksieae, and the generaDeclieuxia andHindsia. The tribesKnoxieae, Anthospermeae, Argostemmateae, Paederieae, Theligoneae, Rubieae, Hedyotideae, andSpermacoceae are members of one clade. TheKnoxieae are monophyletic ifOtiophora, Otomeria, andPentas are included. The tribeAnthospermeae is supported as monophyletic, but its subtribes are not. ThePaederieae, together withTheligonum, form a paraphyletic grade basal to theRubieae. TheHedyotideae, includingSchismatoclada, form a grade at the base of theSpermacoceae. TheGaertnereae are monophyletic and distinct from thePsychotrieae. TheMorindeae are monophyletic and includeDamnacanthus andMitchella. Schradera is the sister group of theMorindeae. ThePsychotrieae are monophyletic when theGaertnereae, Lasianthus, andDeclieuxia are excluded. The recognition of a subtribeHydnophytineae leaves the rest of thePsychotrieae paraphyletic.Psychotria is paraphyletic with respect to all other genera of the tribe. Approximately 50 genera are here classified for the first time based on molecular data.

The rps 16 intron and the phylogeny of the Rubioideae ( Rubiaceae )

DNA sequences from the chloroplast trnL-F region of 154 Rubiaceae and 11 outgroup taxa were analyzed cladistically. An emphasis was placed on the tribes Rondeletieae, Sipaneeae, and Condamineeae. Sipaneeae are not close to Rondeletieae and belong in the Ixoroideae. There is no support for a widely distributed Rondeletieae in a broad sense. Instead, Rondeletieae sensu stricto form an almost entirely Antillean clade. Support was found for the separation of Arachnothryx, Rogiera, Roigella, and Suberanthus from Rondeletia. The Guettardeae as well as Gonzalagunia are found close to a complex formed by Arachnothryx, Javorkaea, and Rogiera. Condamineeae, in a strict sense, belongs in the Ixoroideae. A number of Rondeletieae genera should be transferred to Condamineeae or other parts of Ixoroideae. Support is found for an emended tribe Naucleeae, comprising several genera with spherical pseudanthia. For the first time, tribal or subfamilial affiliation based on molecular sequence data is suggested for Allenanthus, Blepharidium, Chione, Coutaportla, Dolichodelphys, Mazaea, Neobertiera, Neoblakea, Phialanthus, Phyllacanthus, Phyllomelia, Schmidtottia, and Suberanthus.

A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae.

A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae

Summary In both folk taxonomy and science, the idea of species is based on the observation that phenotypic variation is discrete and not continuous. The definition of the species category, the "what," must therefore be restricted to these empirically demonstrable facts. To avoid circularity, concepts about the biological nature of species, the "whys," must be kept separate from the criteria by which individual species are circumscribed. Such ideas are models and can only be judged in terms of their capacity to bring observations into a meaningful context. The Biological Species Concept (BSC), the Evolutionary Species Concept (EvSC) and the Ecological Species Concept (EcSC) are models, not definitions. The BSC has its principal flaw in its inability to deal with uniparentally reproducing organisms. It fails to identify the driving force of speciation. It therefore fails to predict diversity and to explain why different species have different reproductive strategies. The EvSC fails to explain why different lineages are phenetically different. It fails, therefore, to explain why species arise, and why there are differences in diversity and reproductive strategies. The EcSC has the potential to make a direct connection between environment and phenetic variation patterns. It provides a useful conceptual framework for experimentation and observation at the interface between taxonomy and ecology and has the potential to explain on a universal basis variation in diversity and reproductive patterns. In some taxonomically difficult cases it also sheds light on the nature of variation patterns and might therefore help in taxonomic judgment where the BSC is conceptually inapplicable and the EvSC fails to provide useful concepts.

https://www.jstor.org/stable/pdfplus/1223084.pdf

The driving force: species concepts and ecology

Circumscription of the tribeCinchoneae (Rubiaceae) is reconsidered on the basis of a cladistic analysis of structural data comprising 48 characters (164 states). It is concluded that the tribeCinchoneae, in order to be monophyletic, should be restricted to compriseCapirona, Cephalodendron, Cinchona, Cosmibuena, Dolicholobium, Ferdinandusa, Joosia, Ladenbergia, Macrocnemum, andRemijia. It is also suspected, on insufficient evidence, thatMaguireocharis, Pimentelia, andStilpnophyllum belong here.Alseis, Calycophyllum, Schizocalyx, andWittmackanthus form a monophyletic group possibly related to theCinchoneae. A new tribe,Calycophylleae, is proposed to accommodate them.Hillia, which is possibly the sister group of theCinchoneae, is retained in a separate tribe.Coptosapelta, Corynanthe, Crossopteryx, Hymenodictyon, Luculia, Mitragyna, Mussaendopsis, Paracorynanthe, Pausinystalia, andUncaria are referred to the same tribe, for which the nameCoptosapelteae has to be adopted. Probably alsoGreeniopsis belongs here. The generaCigarilla, Coutarea, andExostema, and possiblySyringantha andWernhamia, seem to be most closely related toPortlandia and should be transferred to the tribeCondamineeae. Bouvardia, Coursiana, Danais, Duidiana, Dunnia, Heterophyllaea, Hindsia, Lecanosperma, Manettia, Merumea, Neohymenopogon, andSchismatoclada should be provisionally transferred to the tribeHedyotideae, which is suspected to be polyphyletic, however. No conclusive results were reached concerning the position ofBalmea, Blepharidium, Emmenopterys, andSuberanthus, the position of them remaining uncertain.

Lennart Andersson

Papers

The rps 16 intron and the phylogeny of the Rubioideae ( Rubiaceae )

A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae.

A trnL-F cpDNA sequence study of the Condamineeae-Rondeletieae-Sipaneeae complex with implications on the phylogeny of the Rubiaceae

The driving force: species concepts and ecology

Circumscription of the tribe Cinchoneae (Rubiaceae)―a cladistic approach