Darwin's panoramic view of biology encompassed two metaphors: the phylogenetic tree, pointing to relatively linear (and divergent) complexity, and the tangled bank, pointing to reticulated (and convergent) complexity. The emergence of phylogenetic systematics half a century ago made it possible to investigate linear complexity in biology. Assumption 0, first proposed in 1986, is not needed for cases of simple evolutionary patterns, but must be invoked when there are complex evolutionary patterns whose hallmark is reticulated relationships. A corollary of Assumption 0, the duplication convention, was proposed in 1990, permitting standard phylogenetic systematic ontology to be used in discovering reticulated evolutionary histories. In 2004, a new algorithm, phylogenetic analysis for comparing trees (PACT), was developed specifically for use in analyses invoking Assumption 0. PACT can help discern complex evolutionary explanations for historical biogeographical, coevolutionary, phylogenetic, and tokogenetic processes.

For recently derived species and when the time separating speciation events is short, the phylogenetic distribution of taxa in a gene tree may not accurately reflect the actual species relationships. The phylogenetic tradition of relying on gene tree and species tree synonymy is not reliable under such historical scenarios. Nevertheless, recent studies have demonstrated that accurate estimates of species relationships are possible when the method of phylogenetic inference considers not only the stochastic processes of nucleotide substitution, but also the random loss of gene lineages by genetic drift—even when there is widespread incomplete lineage sorting. This simulation study examines how the broader phylogenetic context, that is, the species tree topology and branch lengths, influences the ability to recover species relationships when taxa have undergone a recent and rapid radiation. As expected, the time since species divergence and the time between speciation events influences whether phylogenetic relationships are accurately estimated. However, the influence of the timing of divergence on the ability to recover species relationships accurately differed depending on the relative position of the taxa in the species tree. Differences in the ability to recover these relationships across multiple simulated species trees highlight the potential effects of taxon sampling on phylogenetic inference at, or near, the species boundary and under high rates of speciation. By focusing attention on the species tree, rather than on the individual gene trees as the basis for interpretations about species relationships, these results also represent a fundamental shift from the phylogenetic paradigm.

Diadromy, broadly defined here as the regular movement between freshwater and marine habitats at some time during their lives, characterizes numerous fish and invertebrate taxa. Explanations for the evolution of diadromy have focused on ecological requirements of individual taxa, rarely reflecting a comparative, phylogenetic component. When incorporated into phylogenetic studies, center of origin hypotheses have been used to infer dispersal routes. The occurrence and distribution of diadromy throughout fish (aquatic non-tetrapod vertebrate) phylogeny are used here to interpret the evolution of this life history pattern and demonstrate the relationship between life history and ecology in cladistic biogeography. Cladistic biogeography has been mischaracterized as rejecting ecology. On the contrary, cladistic biogeography has been explicit in interpreting ecology or life history patterns within the broader framework of phylogenetic patterns. Today, in inferred ancient life history patterns, such as diadromy, we see remnants of previously broader distribution patterns, such as antitropicality or bipolarity, that spanned both marine and freshwater habitats. Biogeographic regions that span ocean basins and incorporate ocean margins better explain the relationship among diadromy, its evolution, and its distribution than do biogeographic regions centered on continents.

Organisms with complex life histories and unusual modes of genome inheritance can present challenges for phylogenetic reconstruction and accurate assessment of biological diversity. This is particularly true for freshwater bivalves in the family Unionidae because: (1) they have complex life cycles that include a parasitic larva and obligate fish host; (2) they possess both a male and female mitochondrial genome that is transmitted through doubly uniparental inheritance (DUI); and (3) they are found in riverine habitats with complex hydrogeological histories. Examination of mitochondrial DNA (mtDNA) sequences, conglutinate morphology, and host fish compatibility of the western fanshell Cyprogenia aberti (Conrad, 1850) revealed significant character variation across its range. Although variation was correlated among the different data sets and supports discrete groups, these groups did not always correspond to geographically isolated populations. Two discrete mtDNA clades exist sympatrically within most C. aberti populations, and these same clades are also diagnosed by at least one morphological character, egg color. The surprisingly high genetic distance (14.61%–20.19%) between the members of these sympatric clades suggests heritance infidelity of the two different mitochondrial genomes. This hypothesis was tested and falsified. More general patterns in geography were observed in host fish compatibility. Populations of C. aberti from the major river systems differed in their ability to utilize fish species as hosts. These differences in reproductive traits, which are presumably genetically based, suggest that these populations are not ecologically exchangeable with one another and represent biological diversity not previously recognized within Cyprogenia Agassiz, 1852.

Pollinators have long been implicated in plant speciation. Peter Raven's earlier work was instrumental in integrating foraging energetics of animals into our understanding of how shifts in major pollinators influence the evolutionary diversification of floral traits. More recently, efforts by Raven and others in the area of conservation have inspired pollination biologists to consider the implications of pollinator shifts and losses due to human activities. This paper uses the shift between hummingbird and hawkmoth pollination as a model for exploring impacts of pollinator shifts on plant populations. Recent studies have quantified the degree of reproductive isolation due to such pollinators in several genera. Data from Ipomopsis Michx. further allow us to consider whether recent changes in pollinator regimes have demographic consequences for plant populations. A majority of plant populations may currently suffer from pollen limitations on seed production, but few data exist on the demographic consequences of poor reproduction. In Ipomopsis, reduced seed production due to pollen limitation can impact the number of individuals surviving to reproduce in the next generation. Some populations of I. tenuituba (Rydb.) V. E. Grant are estimated to have finite rates of increase less than unity, which can be explained in part by current low levels of hawkmoth pollination. In the absence of an increase in hawkmoths, selection for wider corolla tubes and other floral traits could, in principle, attract enough hummingbird pollination to result in a growing population, but models show that such evolution by natural selection may leave the population vulnerable to local extinction. We need more studies of the quantitative demographic consequences of changes in pollinator regimes. Such studies should consider how evolutionary changes influence the risk of extinction.

Systematics and evolutionary biology are being bolstered by a renaissance in cytogenetics and comparative genomics as illustrated by reviewing Peter Raven's integration of cytogenetics and phylogenetics and by presenting updates to his work in three key research areas. The first area is the evolution of chromosomes during the origin of the angiosperms. Raven's analysis of chromosome numbers in the Annonales and other basal angiosperms inspired modern genomic comparisons that have revealed paleopolyploid events, which appear to have occurred early and often during flowering plant diversification. Second, Raven's characterization of chromosome evolution in various genera of Onagraceae is updated in light of a contemporary Onagraceae phylogeny. The possible construction of ancestral karyotypes in the Onagraceae is feasible using techniques that have been successful in analyses of genomic blocks in the Poaceae and Brassicaceae. Third, Raven's work on catastrophic speciation identified the importance of chromosomal rearrangements in the evolution of Clarkia Pursh and the ability of new species to inhabit different environments. Current work in Brassica L. has shown that phenotypic changes contributing to speciation events can arise from relatively few chromosomal rearrangements. A fusion of systematics and cytogenetics is opening new areas of research, with phylogenomics allowing ancestral genome reconstruction, the incorporation of genome-level characters into phylogenetic analyses, and new theories about evolution on a genomic scale.

A revision of the genus Roldana La Llave (Asteraceae: Senecioneae) is given, including a key to species and complete nomenclature with synonymies, description, distribution, and discussion sections for 48 species; eight varieties are recognized and 11 new combinations are made, including one species transfer to the genus Psacaliopsis H. Rob. & Brettell. A phytogeography section for the genus, which is distributed throughout the highlands of Mexico and Central America, with one species entering the southwestern-most U.S.A., is also included. New combinations are established for R. acutangula (Bertol.) Funston, R. aliena (B. L. Rob. & Seaton) Funston, R. hartwegii var. carlomasonii (B. L. Turner & T. M. Barkley) Funston, R. hartwegii var. durangensis (H. Rob. & Brettell) Funston, R. hartwegii var. subcymosa (H. Rob.) Funston, R. kerberi var. calzadana (B. L. Turner) Funston, R. kerberi var. manantlanensis (R. R. Kowal) Funston, R. petasitis var. cristobalensis (Greenm.) Funston, R. petasitis var. oaxacana (Hemsl.) Funston, R. petasitis var. sartorii (Sch. Bip. ex Hemsl.) Funston, as well as for the excluded taxon P. pinetorum (Hemsl.) Funston & Villaseñor. Neotypes are designated for Cineraria platanifolia Schrank, R. ehrenbergiana (Klatt) H. Rob. & Brettell, R. lobata La Llave, R. petasitis (Sims) H. Rob. & Brettell, Senecio acerifolius K. Koch, S. canicidus Sessé & Moc., and S. prainianus A. Berger. Lectotypes are designated for Cacalia nutans Sessé & Moc., C. peltata Sessé & Moc., P. pinetorum, R. albonervia (Greenm.) H. Rob. & Brettell, R. aschenborniana (S. Schauer) H. Rob. & Brettell, R. gilgii (Greenm.) H. Rob. & Brettell, R. heracleifolia (Hemsl.) H. Rob. & Brettell, R. heterogama (Benth.) H. Rob. & Brettell, R. kerberi (Greenm.) H. Rob. & Brettell, R. langlassei (Greenm.) H. Rob. & Brettell, R. lanicaulis (Greenm.) H. Rob. & Brettell, R. petasitis var. cristobalensis, R. petasitis var. sartorii, S. brachyanthus Greenm., S. chapalensis var. areolatus Greenm., S. chrismarii Greenm., S. ghiesbreghtii Regel var. pauciflorus J. M. Coult., S. grandifolius Loes. var. glabrior He

Se presenta una revisión del género Junellia Moldenke, nom. cons. El género comprende 39 especies y seis variedades distribuidas en América del Sur, desde Perú y Bolivia hasta la Argentina y Chile. Se establece un reordenamiento de las categorías infragenéricas a nivel de secciones; se cambia de subgénero Junellia subgén. Thryothamnus (Phil.) Botta secc. Junelliopsis Botta, dándose la siguiente nueva combinación: Junellia subgén. Junellia secc. Junelliopsis (Botta) P. Peralta & Múlgura; y se funda una nueva sección para las especies excluidas de Junellia subgén. Thryothamnus secc. Junelliopsis: Junellia subgén. Thryothamnus secc. Dentium P. Peralta & Múlgura. Las siguientes secciones y series se sinonimizan: Junellia subgén. Thryothamnus secc. Junelliopsis Botta, Verbena L. secc. Junellia (Moldenke) Tronc. ser. Minutifoliae Tronc., Verbena secc. Junellia ser. Thymifoliae Tronc., Verbena secc. Verbenaca Walp. ser. Erinaceae Walp., Verbena secc. Verbenaca ser. Seriphioideae Walp. y Verbena ser. Pauciflorae Briq. Se neotipifican: Verbena juniperina Lag., V. ligustrina Lag., V. minima Meyen, V. thymifolia Lag., V. tridactylites Lag. y V. tridens Lag. Se lectotipifican: Diostea filifolia Miers, V. asparagoides Gillies & Hook. ex Hook., V. bisulcata Hayek, V. connatibracteata Kuntze, V. digitata Phil., V. lorentzii Niederl. ex Hieron., V. ourostachya Briq., V. pygmaea R. E. Fr., V. selaginoides Kunth ex Walp., V. spathulata Gillies & Hook. ex Hook. var. grandiflora Schauer, V. spathulata var. parviflora Schauer y V. uniflora Phil. var. glabriuscula Kuntze. Se transfieren a la sinonimia los siguientes taxones: Junellia echegarayi (Hieron.) Moldenke var. cordifolia Moldenke, J. echegarayi var. puberulenta Moldenke [= J. echegarayi], J. spathulata (Gillies & Hook. ex Hook.) Moldenke var. grandiflora (Schauer) Botta [= J. spathulata var.