The current picture of the history of taxonomy incorporates A. J. Cain's claim that Linnaeus strove to apply the logical method of definition taught by medieval followers of Aristotle. Cain's argument does not stand up to critical examination. Contrary to some published statements, there is no evidence that Linnaeus ever studied logic. His use of the words “genus” and “species” ruined the meaning they had in logic, and “essential” meant to him merely “taxonomically useful.” The essentialism story, a narrative that has most pre-Darwinian biologists steeped in the world view of Plato and Aristotle, is ill-founded and improbable.

How many species one recognizes within a given taxon remains a difficult question, especially when morphology is relatively stable or when clinal variation is present, thus complicating diagnosis. I accept the general lineage concept of species, and my goal is to recognize historically distinct evolutionary lineages that are likely to remain distinct. Here I analyze this task with respect to patterns of species formation in two genera of plethodontid salamanders in California. Ensatina is a ring species complex surrounding the Central Valley of California. At present it is a single species with seven subspecies that are linked by apparent clinal variation in intergrade zones, but there are also some narrow hybrid zones where morphologically and ecologically differentiated forms interact. In contrast, Batrachoseps, which has much the same distribution, has about 20 species in California, most occurring in sympatry with Ensatina. Divergence in the two taxa is based on two fundamentally different phenomena, and yet there are some common themes. Adaptive divergence in coloration is the dominant theme in Ensatina, whereas differentiation is largely perceived at the molecular level in Batrachoseps. Yet both have evolved in the same region and have been affected by many of the same climatic and earth historical phenomena. Within the Ensatina complex, different adaptations related to predator avoidance have evolved. Coloration has diverged in different directions in coastal and inland populations, even though genetic interactions continue to take place. Where coastal populations meet other coastal populations, ecologically and morphologically similar populations merge genetically, even if well differentiated in molecular traits. In contrast, where the ring is crossed and where ecologically and morphologically differentiated populations meet, they hybridize narrowly or are sympatric and behave as if they are species. Within the ring-like distribution, clinal patterns of variation occur. The current polytypic taxonomy is retained, even though it is problematic, because alternatives are even less appropriate. In contrast, where genetically differentiated populations of Batrachoseps meet they typically do not merge. Instead, they replace one another spatially, in part because they are so similar ecologically. Apparently the periods of isolation were sufficiently long that even in the absence of adaptive divergence there has been divergence of isolating mechanisms. Analysis of patterns of genetic differentiation in allozymes and mtDNA in relation to the geological history of California is used to generate biogeographic scenarios to help explain the contrast between Batrachoseps and Ensatina.

Caribbean Anolis lizards are a classic case of adaptive radiation, repeated four times across islands of the Greater Antilles. On each island, very similar patterns of evolutionary divergence have occurred, resulting in the evolution of the same set of ecological specialists—termed ecomorphs—on each island. However, this is only part of the story of the Caribbean anole radiations. Indeed, much of the species diversity of Caribbean Anolis occurs within clades of ecomorphs, which contain as many as 14 ecologically-similar species on a single island. We ask to what extent the classic model of ecological interactions as the driving force in adaptive radiation can account for this aspect of anole evolutionary diversity. Our answer is that it can in part, but not entirely. More generally, the most complete understanding of evolutionary diversification and radiation is achieved by studying multiple hierarchical evolutionary levels from clades to populations.

Hybrid speciation refers to the establishment of novel hybrid genotypes that are reproductively isolated from their parental species and genetically stabilized. Most frequently, reproductive isolation is achieved via an increase in ploidy. However, in some instances new hybrid species arise and become reproductively isolated without a change in chromosome number, a process known as diploid or “homoploid” hybrid speciation. The annual sunflowers of the genus Helianthus provide a well-studied example of this latter mode of speciation. Here, I review this work, placing individual studies in their proper context. These include (1) computer simulations that describe the evolutionary conditions under which hybrid speciation is most likely; (2) molecular phylogenetic studies that document the origins of three hybrid sunflower species; (3) comparative genetic mapping studies that describe the karyotypic changes associated with hybrid speciation; (4) experimental re-creations of homoploid hybrid species that allow genotypic and phenotypic comparisons between synthetic and ancient hybrid lineages; (5) quantitative trait locus (QTL) studies that describe the genetic basis of phenotypic differences between the parental species and the mode of gene action underlying the generation of extreme phenotypes in hybrids; (6) phylogeographic studies that estimate the ages and number of origins of each hybrid species; (7) selection studies that measure the strength of selection on individual traits and QTLs in synthetic hybrids transplanted into hybrid habitats; and (8) candidate gene studies that search for correlations between candidate genes for ecological divergence and traits and QTLs shown to be under selection in the habitats of the hybrid species. Ongoing work includes searches for the molecular signature of selection during hybrid speciation, surveys of gene expression shifts associated with hybrid speciation, and experiments that evaluate the role of new hybrid gene combinations versus reproductive isolation in the ecological divergence of hybrid lineages.

A multi-disciplinary approach, including phylogenetic analysis, population biology, and quantitative genetics, has helped to elucidate the selective factors that have promoted speciation and shifts in breeding systems in Schiedea (Caryophyllaceae). Schiedea is the fifth largest lineage in the native Hawaiian flora and the most diverse lineage with respect to breeding systems. The genus is monophyletic and shares a common ancestor with a clade consisting of two arctic or boreal-north temperate species. Most inter-island colonizations were from older to younger islands, and most movement between islands led to sufficient isolation to result in formation of new species that are single-island endemics rather than species with multi-island distributions. Closely related species pairs occurring on older islands tend to differ in habitat and are isolated ecologically on the same island, while species pairs on younger islands tend to be in similar habitat on different islands. Speciation within this lineage has been associated with shifts in habitat, pollination system, and breeding system, including evolution of selfing (obligate autogamy, facultative autogamy), mixed mating systems, and dimorphism (gynodioecy, subdioecy, and dioecy). Dimorphic breeding systems appear to have been derived independently twice in Schiedea, and facultative autogamy and obligate autogamy have both evolved three times. The colonization of windy, dry habitats appears to occur before changes in sex allocation patterns, and the evolution of dimorphism in this lineage has been promoted by the combination of high inbreeding depression and high selfing rates. Many morphological traits associated with allocation to male and female function are highly heritable, and genetic correlations in general do not appear to constrain the evolution of dimorphism in Schiedea.

Jens C. Clausen, David D. Keck, and William M. Hiesey's biosystematic research on continental tarweeds (Madiinae; Compositae) provided diverse examples of evolutionary change for Clausen's synthesis, Stages in the Evolution of Plant Species. Subsequent anatomical work by Sherwin Carlquist demonstrated that the tarweed lineage also includes a spectacular example of adaptive radiation, the Hawaiian silversword alliance. Molecular phylogenetic data and evidence from genetic and hybridization studies have allowed additional perspectives on Clausen et al.'s and Carlquist's hypotheses of tarweed–silversword evolution. In Californian Layia, Clausen et al.'s evidence for gradual allopatric diversification for the n = 7 taxa accords with patterns of molecular divergence and decay of interfertility across lineages inferred from a rate-constant rDNA tree. In contrast, recent evidence on patterns and timing of diversification in an n = 8 Layia clade indicates multiple examples of accelerated phenotypic evolution, unresolved by Clausen et al., that evidently reflect rapid "budding off" of morphologically distinct lineages in ecologically novel settings. In rDNA trees of Californian Holocarpha, lineages representing different cryptic biological species, documented by Clausen, appear to predate the origin of a morphologically and ecologically distinctive taxon (H. macradenia (DC.) Greene) that retains interfertility with relatives of ancestral phenotype; at fine-scale levels of divergence, a disconnect is evident between evolution of intrinsic, post-mating reproductive barriers and phenotypic evolution in Holocarpha. Clausen's evidence for strong intersterility barriers between the mostly annual, continental species of the “Madia” lineage contrasts with Gerald D. Carr and Donald W. Kyhos's subsequent finding of partial to full interfertility between the phenotypically disparate, insular species of the Hawaiian silversword alliance, a monophyletic group that descended from continental ancestors in the “Madia” lineage. Molecular phylogenetic data indicating major ecological changes associated with diversification, a brief timeframe for diversification, and a shift to woodiness in the ancestry of the silversword alliance uphold Carlquist's hypothesis of adaptive radiation of the group and help explain the lack of substantial, internal barriers to gene flow across lineages therein. Results of recent investigations have shown that highly dynamic evolutionary change in Madiinae, both in phenotypic characters and in modes and patterns of diversification, extends to even finer-scale evolutionary levels than indicated by Clausen et al.'s elegant studies. In general, current evidence on diversification in Madiinae appears to be consistent with Clausen et al.'s views concerning the importance of ecological factors in incipient evolutionary divergence. Phylogeny of Madiinae is no longer the intractable problem perceived by Clausen; relatively little is known about the biological basis for the extreme evolutionary propensities of tarweeds.

The adaptive radiation of Darwin's finches in the Galapagos archipelago stands as a model of species multiplication. The radiation began two to three million years ago, and resulted in 14 species being derived from the original colonizing species. This system is highly suitable for investigating the causes of speciation because closely related species occur sympatrically in several combinations and in environments with relatively little anthropogenic disturbance. The role of natural selection and adaptation to feeding niches in the allopatric phase of speciation has been demonstrated repeatedly. In the sympatric phase of speciation, differences in song and morphology act as a premating barrier to gene exchange. This form of reproductive isolation evolves at least partly as a passive consequence or byproduct of adaptive divergence in beak morphology. Song characteristics diverge in allopatry, largely independent of beak morphology and for a variety of reasons, not all of which are well understood. The barrier to gene exchange in sympatry is not completely effective, however; species hybridize rarely, and under some circumstances the hybrids are surprisingly fit. These results challenge some current notions of species. For example, the ground finch species Geospiza scandens Gould and G. fortis Gould on the island of Daphne Major have lost morphological diagnosability, as a result of introgressive hybridization, while retaining vocal diagnosability. Speciation is a process of divergence, and therefore these two populations are currently despeciating. With a change in climatic conditions they are expected to respeciate. Such merge-and-diverge dynamics may occur frequently in hybrid zones and in relatively young radiations in habitats subject to strong environmental fluctuations.

The genus Guettarda (Guettardeae–Rubiaceae) comprises approximately 150 species, ranging from eastern Africa through the islands of the Indian and Pacific Oceans to the Neotropics. Sequence data from the nuclear ribosomal DNA internal transcribed spacer (ITS) region were used to test the monophyly of Guettarda and its relationships to closely related genera within Guettardeae. The results indicate that Guettarda and two smaller genera, Antirhea and Stenostomum, are polyphyletic. Most Guettarda species fall into two distinct groups: a Neotropical lineage that also includes the widespread Indo-Pacific strand species G. speciosa (the type of the genus), and a New Caledonian lineage that, along with Antirhea and Timonius, comprises a dioecious Paleotropical clade. The Hawaiian endemic Bobea, traditionally considered close to Timonius and assumed to be of Old World origin, appears to be more closely related to Neotropical Guettarda species, suggesting that dioecy may have evolved twice within the tribe. The use of traditional gynoecium characters to delimit genera within Guettardeae is not congruent with the ITS phylogeny; other features, such as inflorescence architecture, sexual system, and palynology, appear to correlate more closely with the molecular phylogeny.

A systematic revision of Capparis sect. Capparis, from western and Central Asia, North Africa, and Europe, is presented here. The taxonomy of this section has been approached combining morphological, biogeographical and molecular data when available. Ten species are recognized, including two new species, Capparis atlantica and C. zoharyi. In addition, four new subspecies are presented: Capparis ovata subsp. myrtifolia, C. parviflora subsp. sphaerocarpa, C. sicula subsp. mesopotamica, and C. sicula subsp. sindiana. Lectotypes are designated for C. aegyptia, C. hereroensis, C. mucronifolia, C. elliptica, C. mucronifolia Boiss. subsp. rosanoviana, C. rupestris, C. ovata, C. parviflora, C. spinosa var. canescens, C. sicula subsp. herbacea, and C. sicula subsp. leucophylla. A full taxonomic treatment, keys, and distribution maps of the recognized species are provided. The two new species are illustrated.

The new outline of relationships in basal branches of the family Compositae Giseke confirms that the sister group to the tribe Cardueae Cass. are not Mutisieae Cass., but rather a group of African genera now classified as the tribe Tarchonantheae Kostel. This change implies that the monophyly of the Cardueae must be reassessed on a molecular basis. Moreover, new collections in recent years allow us to extend our sampling to 70 of the 74 genera of the tribe. We performed a new molecular study of the tribe using one nuclear region (ITS) and two chloroplastic markers (trnL-trnF and matK) in addition to a more appropriate outgroup. Our results confirm that the Cardueae is a natural group but indicate some changes in subtribal delineation: the subtribe Cardopatiinae Less. is recognized and some genera are moved to other subtribes (Myopordon Boiss., Nikitinia Iljin, Syreitschikovia Pavlov, and the Xeranthemum L. group). A recapitulation of a number of interesting questions that remain unresolved in the classification of some large genera is presented.