Causal mechanisms of evolution and the capacity for niche construction

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved.     

Combining environmental niche models,multi-grain analyses,and species traits identifies pervasive effects of land use on butterfly biodiversity across Italy

Understanding how species respond to human activities is paramount to ecology and conservation science, one outstanding question being how large-scale patterns in land use affect biodiversity. To facilitate answering this question, we propose a novel analytical framework that combines environmental niche models, multi-grain analyses, and species traits. We illustrate the framework capitalizing on the most extensive dataset compiled to date for the butterflies of Italy (106,514 observations for 288 species), assessing how agriculture and urbanization have affected biodiversity of these taxa from landscape to regional scales (3–48 km grains) across the country while accounting for its steep climatic gradients. Multiple lines of evidence suggest pervasive and scale-dependent effects of land use on butterflies in Italy. While land use explained patterns in species richness primarily at grains ≤12 km, idiosyncratic responses in species highlighted “winners” and “losers” across human-dominated regions. Detrimental effects of agriculture and urbanization emerged from landscape (3-km grain) to regional (48-km grain) scales, disproportionally affecting small butterflies and butterflies with a short flight curve. Human activities have therefore reorganized the biogeography of Italian butterflies, filtering out species with poor dispersal capacity and narrow niche breadth not only from local assemblages, but also from regional species pools. These results suggest that global conservation efforts neglecting large-scale patterns in land use risk falling short of their goals, even for taxa typically assumed to persist in small natural areas (e.g., invertebrates). Our study also confirms that consideration of spatial scales will be crucial to implementing effective conservation actions in the Post-2020 Global Biodiversity Framework. In this context, applications of the proposed analytical framework have broad potential to identify which mechanisms underlie biodiversity change at different spatial scales.     

Forbidden versus permitted interactions: Disentangling processes from patterns in ecological network analysis

Several studies have identified the tendency for species to share interacting partners as a key property to the functioning and stability of ecological networks. However, assessing this pattern has proved challenging in several regards, such as finding proper metrics to assess node overlap (sharing), and using robust null modeling to disentangle significance from randomness. Here, we bring attention to an additional, largely neglected challenge in assessing species’ tendency to share interacting partners. In particular, we discuss and illustrate with two different case studies how identifying the set of “permitted” interactions for a given species (i.e. interactions that are not impeded, e.g. by lack of functional trait compatibility) is paramount to understand the ecological and co‐evolutionary processes at the basis of node overlap and segregation patterns.     

The extended evolutionary synthesis and human origins: Archaeological perspectives

Recent developments in evolutionary biology have led to a call for an extension of standard evolutionary theory, with its emphasis on processes such as selection and drift, into a much larger theoretical framework that includes processes such as niche construction, developmental plasticity, inclusive inheritance, and developmental bias. Skeptics argue that these processes are already subsumed within the standard theory and thus an extension is not required. Here, we outline what this evolutionary “rethink” might mean for the study of human origins. Specifically, can paleoanthropologists benefit from an extended theoretical toolkit? The papers in this special issue suggest it can be useful but may not be necessary, depending on the kinds of questions that are being asked.     

Modeling Human Ecodynamics and Biocultural Interactions in the Late Pleistocene of Western Eurasia

Given the complex and multidimensional nature of human evolution, we need to develop theoretical and methodological frameworks to account for and model the dynamic feedbacks between co-operational biological and cultural evolutionary systems to better understand the processes that produced modern human behavior. Equally important is the generation of explicit theory-based models that can be tested against the empirical paleoanthropological record. We present a case study that examines evidence for culturally-driven behavioral change among Late Pleistocene hominins that altered the social niche occupied by hominins in western Eurasia, with consequences for subsequent biological and cultural evolution. We draw on a large sample of 167 Pleistocene assemblages across western Eurasia and employ mathematical and computational modeling to explore the feedbacks between cultural and biological inheritance. Shifts in land-use strategies changed the opportunities for social and biological interaction among Late Pleistocene hominins in western Eurasia with a cascade of consequences for cultural and biological evolution, including the disappearance of Neanderthals from the fossil and archaeological records, and the acceleration of cultural evolution among ancestors of modern humans.     

东亚现代人来源的考古学思考:证据与解释

现代人的起源与扩散是当今古人类学界极具争议的问题。目前,"多地区进化"假说和非洲起源为主的"同化"假说是该争议的两大阵营。在"多地区进化"假说的基础上,立足中国的化石材料,吴新智提出了中国乃至东亚古人类"连续演化、附带杂交"的假说,认为中国的现代人主要由本地古老类型人类演化而来。本文从现代人扩散关键时段的考古材料出发,讨论氧同位素5～3阶段(大约13～3万年)考古材料在研究中国现代人形成中的作用和存在的挑战。首先,概括介绍现代人起源的主要假说和现代人扩散的假定路线——南线和北线的多重证据;其次,在此背景下,通过对中国境内考古材料的概括,分析不同石器技术可能反映的现代人来源;最后,简要探讨立足考古材料研究现代人起源与扩散的挑战。总体而言,氧同位素5～3阶段的旧石器考古材料支持中国北方南部和中国南方古人类的连续演化,同时也指示了非洲扩散而出的现代人人群自西北地区和南方地区进入中国的可能性。该模式支持中国古人类"连续演化、附带杂交"假说,然而我们也认识到中国现代人起源研究的考古基础仍十分薄弱,使用考古学材料研究现代人扩散的理论基础也需探讨。目前,细化、完善基础考古数据仍是中国旧石器时代考古学和古人类学学者努力的主要方向之一。如此,我们才能够更加有效地将人类化石与考古学证据融合,进而结合分子生物学的研究,更为全面地理解现代人的起源与演化。     

Semiotic Mechanisms Underlying Niche Construction

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development (sensu stricto) as well as cognitive development and cultural change. In making this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive (i.e., reciprocal). Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior.     

It's Not All Sex and Violence: Integrated Anthropology and the Role of Cooperation and Social Complexity in Human Evolution

Social scientists, especially anthropologists, have long endeavored to understand the evolution of "human nature." This investigation frequently focuses on the relative importance of competition versus cooperation in human evolutionary trajectories and usually results in a primary emphasis on competition, aggression, and even war in attempting to understand humanity. This perspective conflicts with long-standing perspectives in anthropology and some emerging trends and theory in evolutionary biology and ecology. Cooperation and competition are not mutually exclusive in an evolutionary context. As anthropologists, we have demonstrated that humans can–and usually do–get along. Evolution is complex with multiple processes and patterns, not all of which involve competition and conflict. In this article, I summarize elements of modern ecological and evolutionary theory in the context of human cooperative patterns in an attempt to illustrate the valuable role of evolutionary theory and cooperative patterns in integrative anthropological approaches to the human condition.     

Niche construction and the behavioral context of plant and animal domestication

Many animal species attempt to enhance their environments through niche construction or environmental engineering. Such efforts at environmental modification are proposed to play an important and underappreciated role in shaping biotic communities and evolutionary processes. 1 , 2 Homo sapiens is acknowledged as the ultimate niche constructing species in terms of our rich repertoire of ecosystem engineering skills and the magnitude of their impact. We have been trying to make the world a better place—for ourselves—for tens of thousands of years. I argue here that it is within this general context of niche‐construction behavior that our distant ancestors initially domesticated plants and animals and, in the process, first gained the ability to significantly alter the world's environments. The general concept of niche construction also provides the logical link between current efforts to understand domestication being conducted at two disconnected scales of analysis. At the level of individual plant and animal species, on one hand, there recently have been significant advances in our knowledge of the what, when, and where of domestication of an ever‐increasing number of species worldwide. 3 At the same time, large‐scale regional or universal developmental models of the transition to food production continue to be formulated. These incorporate a variety of “macro‐evolutionary” causal variables that may account for why human societies first domesticated plants and animals. 4 , 5 This essay employs the general concept of niche construction to address the intervening question of how, and to connect these two scales of analysis by identifying the general behavioral context within which human societies responded to “macroevolutionary” causal variables and forged new human plant or animal relationships of domestication.     

Operationalizing niche construction theory with stone tools

One of the greatest difficulties with evolutionary approaches in the study of stone tools (lithics) has been finding a mechanism for tying culture and biology in a way that preserves human agency and operates at scales that are visible in the archaeological record. The concept of niche construction, whereby organisms actively construct their environments and change the conditions for selection, could provide a solution to this problem. In this review, we evaluate the utility of niche construction theory (NCT) for stone tool archaeology. We apply NCT to lithics both as part of the “extended phenotype” and as residuals or precipitates of other niche‐constructing activities, suggesting ways in which archaeologists can employ niche construction feedbacks to generate testable hypotheses about stone tool use. Finally, we conclude that, as far as its applicability to lithic archaeology, NCT compares favorably to other prominent evolutionary approaches, such as human behavioral ecology and dual‐inheritance theory.     

HETEROCHRONY AND ALLOMETRY: LESSONS FROM THE WATER STRIDER GENUS LIMNOPORUS

Heterochrony and allometry both deal with evolutionary modifications of ontogenies. Although data about both morphology and age are required to identify heterochronic processes, age data are not needed to study allometry. Using a simple graphical model, we show that allometric patterns cannot be used to infer the underlying heterochronic processes. We present a case study of the water strider genus Limnoporus Stål (Heteroptera: Gerridae) to illuminate the distinct roles that allometry and heterochrony play in integrated studies of the evolution of form. Multivariate analyses reveal several evolutionary modifications of growth trajectories (changes in direction, lateral transposition, and ontogenetic scaling), which are fairly consistent with the hypothesized phylogeny of the genus. Because there is no positive correlation between instar durations and size increments, size cannot be used as a proxy for age data in studies of heterochrony. In fact, a measure of overall size itself shows a remarkable variety of heterochronic changes among the six species. Mixtures of several heterochronic processes predominate over the more unitary reflections of “pure” processes. Heterochronic changes in different branches of the phylogeny, apparently independent of size scaling, suggest considerable potential for adaptive evolution. “Local” differentiation of ontogenetic traits within small clades may be at least as important as “global” evolutionary trends in large clades and will often be missed in “global” analyses.     

Ecomorphological disparity in an adaptive radiation: opercular bone shape and stable isotopes in Antarctic icefishes

To assess how ecological and morphological disparity is interrelated in the adaptive radiation of Antarctic notothenioid fish we used patterns of opercle bone evolution as a model to quantify shape disparity, phylogenetic patterns of shape evolution, and ecological correlates in the form of stable isotope values. Using a sample of 25 species including representatives from four major notothenioid clades, we show that opercle shape disparity is higher in the modern fauna than would be expected under the neutral evolution Brownian motion model. Phylogenetic comparative methods indicate that opercle shape data best fit a model of directional selection (Ornstein–Uhlenbeck) and are least supported by the “early burst” model of adaptive radiation. The main evolutionary axis of opercle shape change reflects movement from a broad and more symmetrically tapered opercle to one that narrows along the distal margin, but with only slight shape change on the proximal margin. We find a trend in opercle shape change along the benthic–pelagic axis, underlining the importance of this axis for diversification in the notothenioid radiation. A major impetus for the study of adaptive radiations is to uncover generalized patterns among different groups, and the evolutionary patterns in opercle shape among notothenioids are similar to those found among other adaptive radiations (three‐spined sticklebacks) promoting the utility of this approach for assessing ecomorphological interactions on a broad scale.     

The need to incorporate human variation and evolutionary theory in forensic anthropology: A call for reform

In 1992, Norm Sauer called for a language shift in which practitioners would move away from the socially loaded term “race” and replace it with the less provocative term “ancestry.” While many heeded the call and moved towards ancestry in their research and reports, the actual approach to research and analysis did not change. In response to this change, there was a large growth in ancestry estimation method development in the early decade of the 2000s. However, the practice of ancestry estimation did not adequately incorporate evolutionary theory in interpretation or trait selection and continued with little critical reflection. In the past decade, there has been an increase in ancestry validation methods with little critique of the “race” concept or discussion of modern human variation or reference samples. To advance, forensic anthropologists need to reckon with the practice of ancestry estimation as it is currently practiced. We are calling for another reform in the axiom focusing on evolutionary theory, population history, trait selection, and population-level reference samples. The practice needs to abandon the terms ancestry and race completely and recalibrate to an analysis of population affinity. Population affinity is a statistical approach based on the underlying population structure that would allow the understanding of how microevolutionary forces act in concert with historical events (e.g., colonization, the Transatlantic Slave Trade, etc.) to shape modern human variation. This is not to be confused with geographic ancestry that all too often can be perceived as interchangeable with social race and as an affirmation of the biological concept of race. It is time to critically evaluate the social and scientific implications of the current practice of ancestry estimation, and re-frame our approach to studying and analyzing modern human variation through a population structure approach.     

The Reproductive Ecology of Industrial Societies,Part I

Is fertility relevant to evolutionary analyses conducted in modern industrial societies? This question has been the subject of a highly contentious debate, beginning in the late 1980s and continuing to this day. Researchers in both evolutionary and social sciences have argued that the measurement of fitness-related traits (e.g., fertility) offers little insight into evolutionary processes, on the grounds that modern industrial environments differ so greatly from those of our ancestral past that our behavior can no longer be expected to be adaptive. In contrast, we argue that fertility measurements in industrial society are essential for a complete evolutionary analysis: in particular, such data can provide evidence for any putative adaptive mismatch between ancestral environments and those of the present day, and they can provide insight into the selection pressures currently operating on contemporary populations. Having made this positive case, we then go on to discuss some challenges of fertility-related analyses among industrialized populations, particularly those that involve large-scale databases. These include “researcher degrees of freedom” (i.e., the choices made about which variables to analyze and how) and the different biases that may exist in such data. Despite these concerns, large datasets from multiple populations represent an excellent opportunity to test evolutionary hypotheses in great detail, enriching the evolutionary understanding of human behavior.     

中国现代人起源与演化的考古学思考

越来越多古人类学和旧石器时代考古学的发现与研究成果极大地改变了我们对现代人类起源、演化和适应理论问题的看法。中国作为东亚一个幅员辽阔的地理区域,已经成为这项研究的热点地带。来自该地区新的人类化石和石器组合对基于非洲和欧亚大陆西部记录构建的“现代人出自非洲说”（Recent Out-of-Africa）提出了挑战。新的古人类学研究结果表明,早期现代人出现于约100 kaBP的中国南方,可能（至少部分）是由那里的土著居民演化而来。一些古老型智人表现出了与早期古人类镶嵌或过渡性的体质特征,并可能与尼安德特人和丹尼索瓦人杂交混合。同时一些遗址出土的打制石器表现出了早期现代人类技术和行为的复杂性。中国北方的小石片石器主工业和南方的砾石石器主工业贯穿于整个更新世,然而从约40 kaBP开始,石叶技术开始出现在中国北部,紧随其后的是这些地区骨制工具和个人装饰品的出现,这表明,更新世晚期西伯利亚和中亚地区与我国北部可能存在着紧密的文化关系,东北亚地区可能存在着由西北向东南的迁移路线。人类化石和考古学证据表明,中国现代人类起源和适应的过程与机制可能与欧亚大陆西部有所不同。本文对有关中国现代人类起源与演化的考古学研究所取得的新发现和进展进行了总体回顾,从考古学角度阐述了对相关重要学术问题的看法,并为未来的研究提出了方向性建议。     

Neandertals,competition, and the origin of modern human behavior in the Levant

The East Mediterranean Levant is a small region, but its paleoanthropological record looms large in debates about the origin of modern humans and the fate of the Neandertals. For most of the twentieth century, the Levantine paleoanthropological record supported models of continuity and evolutionary transition between Neandertals and early modern humans. Recent advances in radiometric dating have challenged these models by reversing the chronological relationship between Levantine Neandertals and early modern humans. This revised chronostratigraphy for Levantine Middle Paleolithic human fossils raises interesting questions about the evolutionary relationship between Neandertals and early modern humans. A reconsideration of this relationship moves us closer to understanding the long delay between the origin of morphologically modern‐looking humans during the Middle Paleolithic (>130 Kyr) and the adaptive radiation of modern humans into Eurasia around the time of the transition from the Middle to Upper Paleolithic (50 to 30 Kyr).     

Developing the genotype-to-phenotype relationship in evolutionary theory: A primer of developmental features

For decades, there have been repeated calls for more integration across evolutionary and developmental biology. However, critiques in the literature and recent funding initiatives suggest this integration remains incomplete. We suggest one way forward is to consider how we elaborate the most basic concept of development, the relationship between genotype and phenotype, in traditional models of evolutionary processes. For some questions, when more complex features of development are accounted for, predictions of evolutionary processes shift. We present a primer on concepts of development to clarify confusion in the literature and fuel new questions and approaches. The basic features of development involve expanding a base model of genotype-to-phenotype to include the genome, space, and time. A layer of complexity is added by incorporating developmental systems, including signal-response systems and networks of interactions. The developmental emergence of function, which captures developmental feedbacks and phenotypic performance, offers further model elaborations that explicitly link fitness with developmental systems. Finally, developmental features such as plasticity and developmental niche construction conceptualize the link between a developing phenotype and the external environment, allowing for a fuller inclusion of ecology in evolutionary models. Incorporating aspects of developmental complexity into evolutionary models also accommodates a more pluralistic focus on the causal importance of developmental systems, individual organisms, or agents in generating evolutionary patterns. Thus, by laying out existing concepts of development, and considering how they are used across different fields, we can gain clarity in existing debates around the extended evolutionary synthesis and pursue new directions in evolutionary developmental biology. Finally, we consider how nesting developmental features in traditional models of evolution can highlight areas of evolutionary biology that need more theoretical attention.     

生态位分化与森林群落物种多样性维持研究展望

一直以来,生态学家和进化生物学家对森林群落物种多样格局及其形成机制持有不同的观点。虽然Robert Ricklefs将进化和生态过程整合的观点已经被群落生态学家广泛接受,但是区域物种进化历史以及局域群落微进化过程是否能够影响群落生态学过程以及这些过程如何影响群落结构和动态还有待商榷。经典的生态位理论同时强调了种间和种内生态位分化对群落多样性维持的影响。但是生态学家普遍认为种间差异足以代表群落内个体间的相互作用关系,并且由于进化过程导致的种内分化往往涉及较长的时间尺度,因此,虽然种内差异是自然选择的重要材料,物种对环境的适应性进化过程所导致的种内分化对群落构建的影响往往被生态学家所忽视。为此,通过回顾种间和个体生态位分化的研究历史,对两类研究分别进行简要阐述,强调在今后的群落生态学研究中需要考虑个体分化对局域群落构建的影响。     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

The origins and detection of plant community structure: Reproductive versus vegetative processes

The exchange of ideas and information between vegetation ecology and pollination ecology is relatively restricted, yet both fields have devised methods to detect the structure of species assemblages and communities. To promote the exchange of ideas between fields I compare approaches, concepts, and problems faced by researchers working in each area. Both vegetative and reproductive interactions may generate assemblage structure through ecological sorting or through character displacement. Vegetative interactions may lead to assemblage organization more often by ecological sorting and reproductive interactions more often by character displacement. Vegetative interactions generally operate over shorter temporal and smaller spatial scales than reproductive interactions and may be affected more strongly by temporal and spatial heterogeneity in abiotic and biotic environments. These differences affect how the concept of ecological niche should be applied to plants. The Hutchinsonian concept of niche needs to be significantly modified before it can be usefully applied to plants. Null models are a valuable tool for investigating both vegetative and reproductive structuring of plant assemblages; however, the procedures followed in the application of null models need further refinement. The appropriate formulation of the null model may require information that is unavailable, hence multiple models may have to be employed to “bracket” conclusions. The literature on pollination community ecology demonstrates that difficult decisions must be made about the likely processes that have generated the structure being tested, the relevant definition of sympatry, how guid membership should be defined and employed, and what constraints should be incorporated into the null model to impose realism. Differences in these decisions will affect the outcome of the analysis. While top-down studies of pattern have numerous advantages, they usually cannot identify the process(es) that have generated the patterns. Bottom-up, experimental studies can be useful for identifying the processes, but they can rarely be used to assess the structure of an entire natural assemblage. The optimal approach to studying assemblage structure is to detect patterns with top-down analysis and use experiments to identify the processes that generate and maintain the patterns.