We review the empirical phylogenetic literature on plant diversification, highlighting challenges in separating the effects of speciation and extinction, in specifying diversification mechanisms, and ...in making convincing arguments. In recent discussions of context dependence, key opportunities and landscapes, and indirect effects and lag times, we see a distinct shift away from single-point/single-cause ‘key innovation’ hypotheses toward more nuanced explanations involving multiple interacting causal agents assembled step-wise through a tree. To help crystalize this emerging perspective we introduce the term ‘synnovation’ (a hybrid of ‘synergy’ and ‘innovation’) for an interacting combination of traits with a particular consequence (‘key synnovation’ in the case of increased diversification rate), and the term ‘confluence’ for the sequential coming together of a set of traits (innovations and synnovations), environmental changes, and geographic movements along the branches of a phylogenetic tree. We illustrate these concepts using the radiation of Bromeliaceae. We also highlight the generality of these ideas by considering how rate heterogeneity associated with a confluence relates to the existence of particularly species-poor lineages, or ‘depauperons.’ Many challenges are posed by this re-purposed research framework, including difficulties associated with partial taxon sampling, uncertainty in divergence time estimation, and extinction.
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Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been ...accomplished in all lineages. Phylogenetic niche conservatism has important consequences for the assembly of both local communities and the regional species pools from which these are drawn. If corridors for movement are available, newly emerging environments will tend to be filled by species that filter in from areas in which the relevant adaptations have already evolved, as opposed to being filled by in situ evolution of these adaptations. Examples include intercontinental disjunctions of tropical plants, the spread of plant lineages around the Northern Hemisphere after the evolution of cold tolerance, and the radiation of northern alpine plants into the Andes. These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity.
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Biome Shifts and Niche Evolution in Plants Donoghue, Michael J; Edwards, Erika J
Annual review of ecology, evolution, and systematics,
11/2014, Volume:
45, Issue:
1
Journal Article
Peer reviewed
Open access
What factors influence whether a lineage can successfully transition into a new biome, and why have some biome shifts been more frequent than others? To orient this line of research we develop a ...conceptual framework in which the likelihood of a biome shift is a function of (
a
) exposure to contrasting environments over time, (
b
) the evolutionary accessibility of relevant adaptations, and (
c
) changing biotic interactions. We evaluate the literature on biome shifts in plants in relation to a set of hypotheses on the size, connectedness, and absolute age of biomes, as well as on the adaptability of particular lineages and ecological interactions over time. We also critique the phylogenetic inference of past biomes and a "global" model-based approach to biome evolution. More robust generalizations about biome shifts will require detailed studies of well-sampled and well-resolved clades, accounting for changes in the relevant abiotic and biotic factors through time.
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Understanding how plants survive drought and cold is increasingly important as plants worldwide experience dieback with drought in moist places and grow taller with warming in cold ones. Crucial in ...plant climate adaptation are the diameters of water-transporting conduits. Sampling 537 species across climate zones dominated by angiosperms, we find that plant size is unambiguously the main driver of conduit diameter variation. And because taller plants have wider conduits, and wider conduits within species are more vulnerable to conduction-blocking embolisms, taller conspecifics should be more vulnerable than shorter ones, a prediction we confirm with a plantation experiment. As a result, maximum plant size should be short under drought and cold, which cause embolism, or increase if these pressures relax. That conduit diameter and embolism vulnerability are inseparably related to plant size helps explain why factors that interact with conduit diameter, such as drought or warming, are altering plant heights worldwide.
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The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. ...Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.
A great tradition in macroevolution and systematics has been the ritual squabbling between palaeontologists and molecular biologists. But, because both sides were talking past each other, they could ...never agree. Practitioners in both fields should play to their strengths and work together: palaeontologists can provide minimum constraints on branching points in the Tree of Life with considerable precision, and estimate the extent of unrecorded prehistory. Molecular tree analysts have remarkable modelling tools in their armoury to convert multiple minimum age constraints into meaningful dated trees. As we discuss here, work should now focus on establishing reasonable, dated trees that satisfy rigorous assessment of the available fossils and careful consideration of molecular tree methods: rocks and clocks together are an unbeatable combination. Reliably dated trees provide, for the first time, the opportunity to explore wider questions in macroevolution.
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Variable rates of molecular evolution have been documented across the tree of life, but the cause of this observed variation within and among clades remains uncertain. In plants, it has been ...suggested that life history traits are correlated with the rate of molecular evolution, but previous studies have yielded conflicting results. Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times. Herbs show much higher rates of molecular change but also much higher variance in rates. Correlates of life history attributes have long been of interest to biologists, and our results demonstrate how changes in the rate of molecular evolution that are linked to life history traits can affect measurements of the tempo of evolution as well as our ability to identify and conserve biodiversity.
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The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, ...and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.
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Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on ...using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here, we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness.
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We present molecular dating analyses for land plants that incorporate 33 fossil calibrations, permit rates of molecular evolution to be uncorrelated across the tree, and take into account ...uncertainties in phylogenetic relationships and the fossil record. We attached a prior probability to each fossil-based minimum age, and explored the effects of relying on the first appearance of tricolpate pollen grains as a lower bound for the age of eudicots. Many of our divergence-time estimates for major clades coincide well with both the known fossil record and with previous estimates. However, our estimates for the origin of crown-clade angiosperms, which center on the Late Triassic, are considerably older than the unequivocal fossil record of flowering plants or than the molecular dates presented in recent studies. Nevertheless, we argue that our older estimates should be taken into account in studying the causes and consequences of the angiosperm radiation in relation to other major events, including the diversification of holometabolous insects. Although the methods used here do help to correct for lineage-specific heterogeneity in rates of molecular evolution (associated, for example, with evolutionary shifts in life history), we remain concerned that some such effects (e.g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences.
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