Michael J. Donoghue’s research while affiliated with Yale University and other places

In a neotropical lineage of the plant clade Viburnum (Adoxaceae) several leaf ecomorphs evolved independently and repeatedly as the group radiated through cloud forests of North and South America. Here, we focus on one pair of co-occurring sister species within this radiation with strongly contrasting leaf morphotypes and document the presence of phenotypically diverse and genetically admixed hybrid individuals in multiple hybrid swarms. Hybrid phenotypes are generally intermediate in form, but sometimes show parental or entirely novel and transgressive combinations of leaf traits, suggesting that parental leaf ecomorphs can be functionally and genetically dissociated. We used admixture mapping within hybrid swarms to investigate the genetic architecture of key traits comprising these leaf ecomorphs and uncovered loci proximal to known genes implicated in leaf development, including some that may alter multiple leaf traits simultaneously, potentially facilitating the emergence of leaf syndromes. We conclude that the shared genetic architecture underlying some traits, such as leaf size and marginal teeth, could promote the repeated evolution of these traits in concert, while low levels of genetic linkage between other leaf traits supports the hypothesis that selection promoted the repeated assembly of particular combinations of leaf traits as Viburnum radiated throughout the neotropics.

Where each species actually lives is distinct from where it could potentially survive and persist. This suggests that it may be important to distinguish established from enabled biome affinities when considering how ancestral species moved and evolved among major habitat types. We introduce a new phylogenetic method, called RFBS, to model how anagenetic and cladogenetic events cause established and enabled biome affinities (or, more generally, other discrete realized versus fundamental niche states) to shift over evolutionary timescale. We provide practical guidelines for how to assign established and enabled biome affinity states to extant taxa, using the flowering plant clade Viburnum as a case study. Through a battery of simulation experiments, we show that RFBS performs well, even when we have realistically imperfect knowledge of enabled biome affinities for most analyzed species. We also show that RFBS reliably discerns established from enabled affinities, with similar accuracy to standard competing models that ignore the existence of enabled biome affinities. Lastly, we apply RFBS to Viburnum to infer ancestral biomes throughout the tree and to highlight instances where repeated shifts between established affinities for warm and cold temperate forest biomes were enabled by a stable and slowly-evolving enabled affinity for both temperate biomes.

A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of Viburnum has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa of have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized as V. seemenii f. minor has recently occupied the drier Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in northern Argentina. Plants in these populations form a well-supported clade with a distinctive genetic signature and they have evolved smaller, narrower leaves. We interpret this as the beginning of a within-species divergence process that has elsewhere in the neotropics resulted repeatedly in Viburnum species with a particular set of leaf ecomorphs. Specifically, the southern populations are in the process of evolving the small, glabrous, and entire leaf ecomorph that has evolved in four other montane areas of endemism. As predicted based on our studies of leaf ecomorphs in Chiapas, Mexico, these southern populations experience generally drier conditions, with large diurnal temperature fluctuations. In a central portion of the range of V. seemenii, characterized by wetter climatic conditions, we also document what may be the initial differentiation of the leaf ecomorph with larger, pubescent, and toothy leaves. The emergence of these ecomorphs thus appears to be driven by adaptation to subtly different climatic conditions in separate geographic regions, as opposed to parapatric differentiation along elevational gradients as suggested by Viburnum species distributions in other parts of the neotropics.

This chapter discusses the principal ways in which botanists have classified plants and some of the reasoning behind those classifications. It discusses the early collections on which plant systematics is based. These collections are intimately connected with European colonial expansion, what price owners of private herbaria were prepared to pay for specimens, and what kind of specimen they preferred. The chapter also describes the history of botanical classification and highlights the longstanding and continuing tension between the makers and the users of classifications. It clarifies how relationships are understood, how nature is visualized, and how higher taxa are delimited.

Plant Systematics begins by looking at the field of plant systematics as a whole. It then introduces methods and principles of biological systematics before turning to the historical background of classification and system in flowering plants. Next, it examines taxonomic evidence, including an outline of structural and biochemical characters. The text also discusses the evolution of plant diversity and provides an overview of green plant phylogeny. Finally, the book ends with an analysis of lycophytes, ferns, and gymnosperm, and phylogenetic relationships of angiosperms.

This chapter considers the lineage of green plants, which is a major lineage that includes the so-called green algae and land plants. It explains that green plants share a number of features, including the presence of the photosynthetic pigments chlorophyll a and b and storage of carbohydrates in the form of starch. The chapter also examines the presence of two anterior whiplash flagella at some stage of the life cycle of green plants. The chapter also covers land plants or embryophytes, whose closest extant relatives are members of the “charophytes,” a green algal group. It traces the life histories of land plants, which involve the alternation of two morphologically distinct bodies, thick-walled spores, an embryonic stage in the life cycle, specialized structures that protect the gametes, and a cuticle.

This chapter traces the origin and evolution of several separately derived plant lineages, thereby putting the green plant lineage into a broad phylogenetic perspective. It focuses on the evolution of green plants and several critical transitions, including the origin of the land plants, vascular plants, seed plants, and flowering plants. It also chronicles the evolutionary events leading up to the mosses, the horsetails, or any other group leading to angiosperms. The chapter depicts phylogenetic relationships among the major branches of the entire tree of life based on recent analyses and explains the broad phylogenetic distribution of photosynthetic organisms. It refers to chloroplasts found in eukaryotes that are endosymbiotic organelles and derived ultimately from a cyanobacterial ancestor.

This chapter describes natural variation among individuals as an essential ingredient of evolution, elaborating how this variation arises and is distributed geographically. The chapter examines processes that create discrete units of variation that are of central interest to systematists, especially those that result in the formation of species. It also analyses mating between individuals of different plant species, blurring the boundary between species. This has little effect on morphological variation within a species. The chapter furthermore discusses interspecific gene flow. This plays a dual role in speciation, which includes reducing diversity by merging species. It highlights speciation when coupled with polyploidy, an important source of genetic variation within plant species.

This chapter concentrates on angiosperms or flowering plants, which are considered the dominant land plants and sister to a group that includes all other extant seed plants. Angiosperms have a long fossil record going back to the earliest Cretaceous period, and they possibly originated during the Jurassic period more than 140 million years ago. The chapter covers the two great groups of angiosperm species: monocots and eudicots. Monocots are plants with a single cotyledon and pollen grains that monosulcate, while eudicots are plants with two cotyledons and pollen grains that predominantly tricolpate. The chapter reviews data from DNA sequences and morphology that show that the monocot and eudicot clades are derived from members of a morphologically disparate, paraphyletic group of families.

The chapter focuses on taxonomic evidence consisting of the characters used in phylogenetic analyses. Plant classifications are based on this evidence, including characters used in describing patterns of variation at or below the species level. The chapter shows how taxonomic evidence can be gathered from a wide variety of sources, from all parts of a plant, and during all stages of a plant's development. It also summarizes the use of characters from morphology, anatomy, embryology, chromosomes, palynology, secondary metabolites, and proteins. The chapter also considers nucleic acids, namely DNA and RNA, as these are an increasingly important source of taxonomic characterization in plant taxonomy and the rapidly developing field of molecular systematics. The chapter also discusses morphological characters, which are used for practical plant identification and hypothesizing phylogenetic relationships.