In 1990 Robert Lickliter and Thomas Berry identified the phylogeny fallacy, an empirically untenable dichotomy between proximate and evolutionary causation, which locates proximate causes in the decoding of ‘ genetic programs’, and evolutionary causes in the historical events that shaped these programs. More recently, Lickliter and Hunter Honeycutt argued that Evolutionary Psychologists commit this fallacy, and they proposed an alternative research program for evolutionary psychology. For these authors the phylogeny fallacy is the proximate/evolutionary distinction itself, which they argue (...) constitutes a misunderstanding of development, and its role in the evolutionary process. In this article I argue that the phylogeny fallacy should be relocated to an error of reasoning that this causal framework sustains: the conflation of proximate and evolutionary explanation. Having identified this empirically neutral form of the phylogeny fallacy, I identify its mirror image, the ontogeny fallacy. Through the lens of these fallacies I attempt to solve several outstanding problems in the debate that ensued from Lickliter and Honeycutt’s provocative article. (shrink)

The use of evolutionary explanations to explain phenomena at the individual level has been described by various authors as an explanatory error, the so-called Phylogeny Fallacy. In this paper, this fallacy will be analyzed in the context of teleosemantics, a central project of the philosophy of mind whose main aim is to naturalize intentional systems by appealing to their biological teleofunctions. I will argue that those teleosemantics projects that invoke evolutionary functions generally commit the fallacy. First, I will point (...) to various arguments in the literature that point to this fallacy. However, a more general argument will also be made. To illustrate this puzzling scenario, I will present two desiderata that any teleosemantic project must fulfill. I will argue that naturalizing intentionality based on natural selection creates an explanatory gap between types and tokens. This gap prohibits an adequate explanation of the desiderata. To close the gap, teleosemantics invokes replicator biology, a view of inheritance that has already been identified to commit the fallacy. This leads teleosemantics into a complex situation: to close the gap, it must commit the fallacy. (shrink)

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

A rational agent has beliefs reflecting the state of its environment, and likes or dislikes Its situation. When it finds the world not entirely to Its liking, it tries to change that. We can, accordingly, evaluate a system of cognition in terms of its probable success in bringing about situations that are to the agent's liking. In doing this we are viewing practical reasoning from “the design stance.” It is argued that a considerable amount of the structure of rationality can (...) be elicited as providing the only apporant solutions to various logical and feasibility problems that arise in the course of trying to design a rational agent that satisfies this design specification. (shrink)

Abstract: The use of evolutionary explanations to account for proximate phenomena has been labeled by various authors as an explanatory error, the so-called phylogeny fallacy. In this paper, this fallacy will be analyzed in the context of teleosemantics. I will discuss whether teleosemantics projects that rely on the Selected-Effect Theory of Functions (i.e., mainstream teleosemantics) generally commit the fallacy. To frame the discussion, I will present two desiderata that, as argued here, every teleosemantic project must fulfill. The actuality desideratum, (...) motivated by Brentano’s problem, demands for a proximate analysis of the properties that make a system intentional. The historical desideratum, on the other hand, says that a teleological view of intentionality requires a historical dimension in order to understand the causal basis of teleological explanations. While I give some reasons why mainstream teleosemantics might be implicated in the phylogeny fallacy, my main argument aims to highlight an explanatory gap in mainstream teleosemantics: the population perspective on teleofunctions is inadequate to explain the proximate properties of intentional systems. In other words, the account of the historical desideratum in population-evolutionary terms prevents an adequate solution to the actuality desideratum. This is related to two central goals of teleosemantics: The goal of explaining content determination by recourse to natural selection processes makes it impossible to solve another goal of teleosemantics, the so-called problem of representational status. I analyze this situation and argue that inherited information (sometimes interpreted in a teleosemantic sense) plays the role of closing the gap. This leads teleosemantics into a complex situation: in order to close the gap, it must commit the fallacy. At the end of the article, I propose an alternative to fulfill both desiderata, motivated by an evo-devo perspective. I state that lineage explanations have the property of providing historical explanations based on proximate causes. (shrink)

The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 γ‐proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While the evolutionary relationships among these (...) species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of γ‐proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species. BioEssays 26:463–468, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Metazoa are one of the great monophyletic groups of organisms. They comprise several major groups of organisms readily recognizable based on their anatomy. These major groups include the Bilateria (animals with bilateral symmetry), Cnidaria (jellyfish, corals and other closely related animals), Porifera (sponges), Ctenophores (comb jellies) and a phylum currently made up of a single species, the Placozoa. Attempts to systematize the relationships of these major groups as well as to determine relationships within the groups have been made for nearly (...) two centuries. Many of the attempts have led to frustration, because of a lack of resolution between and within groups. Other attempts have led to “a new animal phylogeny”. Now, a study by Dunn et al.,1 using the expresssed sequence tag (EST) approach to obtaining high‐throughput large phylogenetic matrices, presents an “even newer” animal phylogeny. There are two major aspects of this study that should be of interest to the general biological community. First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion. BioEssays 30:1043–1047, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

Responses are strengthened by consequences having to do with the survival of individuals and species. With respect to the provenance of behavior, we know more about ontogenic than phylogenic contingencies. The contingencies responsible for unlearned behavior acted long ago. This remoteness affects our scientific methods, both experimental and conceptual. Until we have identified he variables responsible for an event, we tend to invent causes. Explanatory entities such as “instincts,” “drives,” and “traits” still survive. Unable to show how organisms can behave (...) effectively under complex circumstances, we endow them with special abilities permitting them to do so.Behavior exhibited by most members of a species is often accepted as inherited if all members were not likely to have been exposed to relevant ontogenic contingencies. When contingencies are not obvious, it is perhaps unwise to call any behavior either inherited or acquired, as the examples of churring in honey guides and following in imprinted ducklings show. Nor can the relative importance of phylogenic and ontogenic contingencies be argued from instances in which unlearned or learned behavior intrudes or dominates. Intrusions occur in both directions.Behavior influenced by its consequences seems directed toward the future, but only past effects are relevant. The mere fact that behavior is adaptive does not indicate whether phylogenic or ontogenic processes have been responsible for it. Examples include the several possible provenances of imitation, aggression, and communication. The generality of such concepts limits their usefulness. A more specific analysis is needed if we are to deal effectively with the two kinds of contingencies and their products. (shrink)

Locke & Bogin (L&B) rightly point to the absence of ontogeny in theories of language evolution. However, they overly rely upon ontogenetic data to isolate components of the language faculty. Only an adaptationist analysis, of the sort seen in evolutionary psychology, can carve language at its joints and lead to testable predictions about how language works.

I propose conceptualizing stress in standard phylogenetic terms of stress characters, as well as stress phenotypes, as a way to improve stress research involving nonhuman models. PMID: 38626744.

Phylogenies are increasingly being used to investigate human history, diversification and cultural evolution. While using phylogenies in this way is not new, new modes of analysis are being applied to inferring history, reconstructing past states, and examining processes of change. Phylogenies have the advantage of providing a way of creating a continuous history of all current populations, and they make a large number of analyses and hypothesis tests possible even when other forms of historical information are patchy or nonexistent. In (...) common with approaches taken in other historical sciences, phylogenetics is a way of reconstructing past and processes using the traces left in the present day. Trees, based on DNA, language, cultural traits, or other evidence, are now sprouting all over the academic landscape. The increasing use of phylogenetic analysis to understand human cultural evolution has been embraced by some, and scorned by others. The purpose of this article is not to review methods and applications of phylogenetic analyses, nor to consider the growing field of cultural phylogenetics, but, more broadly, to explore how we interpret phylogenies as narratives about human diversification. The first half of the article deals with meaning: phylogenies are often interpreted as histories, but a bifurcating tree is at best an abstract representation of history, and its connections to past events and processes is dependent on the data used, the assumptions made in the analysis, and the degree to which nodes in the tree (where one lineage splits into two) can be connected to change and movement in real populations. The second half of the article explores the purpose of phylogenies: a tree does not have to be a literal history of human lineages in order to be useful for investigating processes of human diversification. Phylogenies should not be read as accurate records of history, but as a way of exploring plausible explanations for current patterns of diversity. Phylogenies provide important information that can be used to test ideas about human diversity, and can help to guard against errors of inference arising from statistical artifacts. (shrink)

This commentary takes issue with Corballis's claim to have presented a falsifiable hypothesis. It argues that Corballis has instead presented a framework of weak inferences that, although unfalsifiable, might help to constrain future theory-building.

The concept that renders morphology a tool for phylogeny reconstruction is homology. The concept of homology is rooted in pre-evolutionary idealistic morphology. The claim that the goal of idealistic morphology was the seriability of form may sound paradoxical given that this discipline proceeded within a framework of strictly delimited types. But the types only demarcate where seriability starts and where it comes to an end. Carl Gegenbaur’s was recognized as a milestone in idealistic morphology. A comparison with the second (...) edition of 1870 illustrates Gegenbaur’s turn to evolutionary morphology. The methodology remained the same–seriability of form–but the series was no longer merely descriptive or conceptual but now a historical, evolutionary one. Gegenbaur emphasized that seriability of form was possible not only between species of the same type, but also between parts of organisms of the same type. Pursuing this project, he found that different parts of organisms evolve at different rates, resulting in an incongruence between the series of parts relative to the series of species under comparison. This incongrence was called chevauchement des spécialisations by Louis Dollo, Spezialisationskreuzungen by Othenio Abel, and heterobathmy of characters by Armen Takhtajan. Willi Hennig, the founder of modern methods in phylogenetic systematics, discovered that the heterobathmy of characters was a precondition for the establishment of the phylogenetic relationships based on shared derived characters. The result was a replacement of the search for ancestors by a search for relative degrees of phylogenetic relationships. (shrink)

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved tree thinking is crucial. The most-serious problem comes from reading trees as ladders from left to right - many biologists assume that species-poor lineages that appear early branching or basal are ancestral - we call this the primitive lineage fallacy. This mistake causes misleading inferences about changes (...) in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21st century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19th century notions about the ladder of progress driving evolution. (shrink)

Some data from earlier work concerning the evolutionary correlation of anthophilous insects, entomophilous plants, herbivorous animals, and natural soil groups are briefly summarized. Presumed successive evolution of plant and animal communities from the early Paleozoic era to the more recent formation of prairies, steppes and other grassland areas is described and pictured in Fig. 6. A definite correlation has been found among the coevolution of flowering plants, pollinating insects, ruminant animals and fertility grades of natural soil groups .Plants, insects, animals (...) and soil are interrelated in evolution as reciprocal selective and regulating factors in certain biotic and abiotic environments. This complex system can be better studied by application of the coenogenic concept and hologenic and syngenic methods.Various stages of the development of an agricultural environment in the prairie areas of the North American plains are briefly described and illustrated in Plates I–VII. A new radical change in the development by the introduction of so-called “Circle Farming” is pictured in Plates VIII–IX. This new irrigated farming system is not only profitable for the increasing of yields, but promises to some extent the restoration of a biologically balanced environment in an extensively cultivated agricultural landscape. (shrink)

During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is (...) possible to predict and represent potential evolutionary trajectories by representing phylogenetic trees into a 3D projection of the sequence space. With the case of the aminodeoxychorismate synthase, an enzyme involved in folate synthesis, we show that this representation raises interesting questions about the complexity of the evolution of a given biological function, in particular concerning its capacity to explore the sequence space. (shrink)

The different aspects of floral evolution—Angiosperm descent, floral morphology and pollination ecology—are discussed on the basis of the anthocorm theory of the angiospermous flower. Opposed ideas are critically compared and rejected mainly on account of several inconsistencies and flaws in old floral concepts. Floral evolution passed from a very early phase of dicliny, anemophily and aphananthy of the anthocorm to a phase of incipient entomophily soon associated with a partial sex reversal within the anthocorm. This second phase culminated in the (...) monoclinous and primarily zoophilous flower types, whereas other floral types, more particularly the primarily anemophilous, diclinous flowers, are the direct descendants of the anthocorms of the initial phase. The second phase gave rise to at least two morphologically different flower types and two separate semophyletic lines of floral evolution , in each of which the primary zoophily is almost always associated with the development of intrafloral semaphylls usually of androecial derivation. Early flower types were aphananthous and clearly anthocormoid and assumed the morphology and other characteristics of a true flower by contractions, condensations, readjustments, oligomerisations, reductions and modifications leading to the great variety of adaptive floral patterns.Divers aspects de l'évolution de la fleur — à savoir la descendance des Angiospermes, la morphologie de la fleur, et l'écologie de la pollination — sont discutés à partir de l'hypothèse florale de l'anthocorme. Les opinions opposées, après d'être comparées et critisées, sont rejetées principalement à cause des inconséquences et inconsistances des anciens théorèmes morphologiques concernant l'origine de la fleur. L'évolution de la fleur commençait avec une phase d'antan de diclinie, anémophilie et aphananthie, et s'avançait graduellement dans la direction d'une phase entomophilique initiale, bientôt accompagnée d'un renversement de sexe partiel à l'intérieur de l'anthocorm. La deuxième phase culminait vers les types florals monoclines avec zoophilie primaire pendant que des autres types florals, particulièrement les fleurs diclines avec anémophilie primaire, sont les descendants directs du stade initiale de l'anthocorme. A partir de la phase II , au moins deux types florals différents et aussi deux sémophylèses florals séparés se développaient. Dans chacun de ses phases III et III A la zoophilie primaire est presque toujours accouplée avec l'origine des sémaphylles intrafloraux le plus souvent dérivés des étamines. Les anciens types des fleurs ayant été aphanantique et au début encore nettement anthocormoïdes , graduellement prenaient la forme d'une des plusieurs types floraux adaptifs par une contraction de l'axe florale et par l'entassement, l'oligomérisation et la modification des pièces de la fleur.Die drei Aspekte der Evolution der Blüte — die Abstammungsgeschichte der Angiospermen, Blütenmorphologie und Bestäubungsökologie — werden, ausgehend von der Anthokormtheorie der Angiospermenblüte, eingehend besprochen. Entgegengesetzte Meinungen werden kritisch verglichen und hauptsächlich auf Grund mehrerer Strittigkeiten und Fehler der älteren blütenmorphologischen Axiomen abgelehnt. Die Evolution der Blüte fing an mit einer frühen Phase mit Diklinie, Anemophilie und Aphananthie des Anthokorms und schritt allmählich weiter in die Richtung von beginnender Entomophilie, bald mit einer partiellen Geschlechtsinversion innerhalb des Anthokorms zusammengehend. Diese zweite Phase kulminierte in den monoklinen und primär zoophilen Blütentypen, während andere Blütengestalten, besonders die primär anemophilen und diklinen Angiospermenblüten, die unmittelbaren Abkömmlinge der Initialphase des Anthokorms sind. Aus der zweiten Phase entwickelten sich wenigstens zwei morphologisch differenzierte Blütenformen und auch zwei geschiedene Blütensemophylesen , in jeder die primäre Zoophilie fast immer verbunden ist mit der Entwicklung von intrafloralen und meistens von Staubblättern angeleiteten Semaphyllen . Die frühen Blütentypen waren aphanantisch und anfänglich noch deutlich anthokormoid und nahmen allmählich die entgültige Gestalt von einer der vielen adaptiven Blütentypen an durch eine Verkürzung der Blütenachse, und durch ein Zusammendrängen, Oligomerisation und Abänderung der Blütenteile. (shrink)

Despite the enormous importance and widespread use of the term, it is unclear exactly what a phylogeny represents. It is important to define phylogeny precisely since other central terms like “clade” and “monophyletic” are often defined relative to phylogenetic trees and on some views in taxonomy, taxa must be clades. Edwards presents the common picture in contemporary systematics as depending on the existence of a “species tree” in which phylogeny “records the branching pattern of evolving lineages through (...) time”. But what, precisely, does this mean? (shrink)

Phylogenetically controlled studies across multiple species correct for taxonomic confounds in physiological performance traits. Therefore, they are preferred over comparisons of two or few closely‐related species. Funding bodies, referees and journal editors nowadays often even reject to consider detailed comparisons of two or few closely related species. Here, we plea for a less dogmatic stance on such comparisons, because phylogenetic studies come with their own limitations similar in magnitude as those of two‐species comparisons. Two‐species comparisons are particularly relevant and instructive (...) for understanding physiological pathways and de novo mutations in three contexts: in a purely mechanistic context, when differences in the regulation of a trait are the focus of investigation, when a physiological trait lacks a direct connection to fitness, and when physiological measures cannot easily be standardized among laboratories. In conclusion, phylogenetic comparative and two‐species studies have different strengths and weaknesses and combining these complementary approaches will help integrating biology. (shrink)

Biology and the social sciences share an interest in phylogeny. Biologists know that living species are descended from past species, and use the pattern of similarities among living species to reconstruct the history of phylogenetic branching. Social scientists know that the beliefs, values, practices, and artifacts that characterize contemporary societies are descended from past societies, and some social science disciplines, linguistics and cross cultural anthropology for example, have made use of observed similarities to reconstruct cultural histories. Darwin appreciated that (...) his theory of descent with modification had many similarities of pattern and process to the already well developed field of historical linguistics. In many other areas of social science, however, phylogenetic reconstruction has not played a central role. (shrink)

We examine the ontogeny and phylogeny of object and fantasy play from a functional perspective. Each form of play is described from an evolutionary perspective in terms of its place in the total time and energy budgets of human and nonhuman juveniles. As part of discussion of functions of play, we examine sex differences, particularly as they relate to life in the environment of evolutionary adaptedness and economic activities of human and nonhuman primates. Object play may relate to foraging (...) activities. Although fantasy play has been viewed as limited to humans, we speculate that certain types of fantasy play may be present in some nonhuman primates. Fantasy play may enable juveniles to see situations from different perspectives. We conclude that fantasy play may have immediate effects and object play may have deferred effects. (shrink)

Phylogenetic trees based on gene sequence data contain information about the evolutionary processes responsible for their genesis. Methods have now been developed which help to reveal those processes. The methods are based on simple models of evolutionary change but, when applied across individuals in a population, rather than across species in a higher‐level taxon, they can reveal the past history of population change. Examples from salamanders and viruses are used to illustrate how the past history of changes in speciation rate (...) and the origin of epidemics can be inferred in the absence of fossil material or historical documentation. (shrink)

Current debates about “Darwinizing culture” have typically focused on the validity of memetics. In this article we argue that meme-like inheritance is not a necessary requirement for descent with modification. We suggest that an alternative and more productive way of Darwinizing culture can be found in the application of phylogenetic methods. We review recent work on cultural phylogenetics and outline six fundamental questions that can be answered using the power and precision of quantitative phylogenetic methods. However, cultural evolution, like biological (...) evolution, is often far from treelike. We discuss the problems reticulate evolution can cause for phylogenetic analyses and suggest ways in which these problems can be overcome. Our solutions involve a combination of new methods for the study of cultural evolution , and the triangulation of different lines of historical evidence. Throughout we emphasize that most debates about cultural phylogenies can only be settled by empirical research rather than armchair speculation. (shrink)

If our knowledge of human cognition were based solely on research with participants younger than the age of 2 years, there would be no basis for the relational reinterpretation hypothesis, and Darwin's continuity theory would be safe as houses. Because many of the shortcomings cited apply to human infants, we propose how a consideration of cognitive development would inform the relational reinterpretation hypothesis.

Recent data have provided evidence for an unrecognised ancient lineage of green plants that persists in marine deep-water environments. The green plants are a major group of photosynthetic eukaryotes that have played a prominent role in the global ecosystem for millions of years. A schism early in their evolution gave rise to two major lineages, one of which diversified in the world's oceans and gave rise to a large diversity of marine and freshwater green algae (Chlorophyta) while the other gave (...) rise to a diverse array of freshwater green algae and the land plants (Streptophyta). It is generally believed that the earliest-diverging Chlorophyta were motile planktonic unicellular organisms, but the discovery of an ancient group of deep-water seaweeds has challenged our understanding of the basal branches of the green plant phylogeny. In this review, we discuss current insights into the origin and diversification of the green plant lineage. (shrink)

Historical language change (), like evolution itself, is a fact; and its implications for the biological evolution of the human capacity for language acquisition () have been ably explored by many contemporary theorists. However, Christiansen & Chater's (C&C's) revolutionary call for a replacement of phylogenetic models with glossogenetic cultural models is based on an inadequate understanding of either. The solution to their lies before their eyes, but they mistakenly reject it due to a supposed Gene/;culture co-evolution poses a series of (...) difficult theoretical and empirical problems that will be resolved by subtle thinking, adequate models, and careful cross-disciplinary research, not by oversimplified manifestos. (shrink)

Defining and measuring biodiversity is an important research area in biology, with very interesting theoretical and applied aspects. Numerous definitions have been proposed, and these definitions of biodiversity influence how it is measured. From the still commonly used measure of species diversity, through higher taxon diversity, molecular measures, ecological measures and indicator taxa, these measures have as their fundamental shortcoming the lack of an explicit consideration of the evolutionary context represented by phylogenies. Attempts have been made to incorporate phylogenetic considerations (...) into measuring biodiversity, but more hypothesis‐driven research needs to be done. A specific case study is presented of how this added emphasis on phylogeny‐based biodiversity measurement can influence the way in which research is directed and hypotheses are generated. The elucidation of the relationship of biodiversity to ecosystem functioning is a very timely concern with the unarguable loss of biodiversity this planet is experiencing, whichever way biodiversity is measured. (shrink)

The small, relatively constant size and conservative evolution of chloroplast DNA (cpDNA) make it an ideal molecule for tracing the evolutionary history of plant species. At lower taxonomic levels, cpDNA variation is easily and conveniently assayed by comparing restriction patterns and maps, while at higher taxonomic levels, DNA sequencing and inversion analysis are the methods of choice for comparing chloroplast genomes. The study of cpDNA variation has already yielded important new insights into the origin and evolution of many agriculturally important (...) crop plants, and promises to significantly enhance our phylogenetic understanding of the major lines of descent among land plants and algae. (shrink)

Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically (...) inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to “boot,” i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell “body” into which genomes are placed. (shrink)

When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the (...) level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori. (shrink)

Gentle handling of mammals , and lizards , but not of frogs and fish elevated the set-point for body temperature, i.e., produced an emotional fever, achieved only behaviourally in lizards. Heart rate, another detector of emotion in mammals, was also accelerated by gentle handling, from ca. 70 b/min to ca. 110 b/min in lizards. This tachycardia faded in about 10 min. The same handling did not significantly modify the frogs’ heart rates. The absence of emotional tachycardia in frogs and its (...) presence in lizards , together with the emotional fever exhibited by mammals and reptiles, but not by frogs or fish, would suggest that emotion emerged in the evolutionary lineage between amphibians and reptiles. Such a conclusion would imply that reptiles possess consciousness with its characteristic hedonic dimension, pleasure. The role of sensory pleasure in decision making was therefore verified in iguanas placed in a motivational conflict. To be able to reach a bait , the iguanas had to leave a warm refuge, provided with standard food, and had to venture into a cold environment. The results showed that lettuce was not necessary to the iguanas and that they traded off the palatability of the bait against the disadvantage of the cold. Thus, the behaviour of the iguanas was possibly produced, as it is in humans, through the maximization of sensory pleasure. Altogether, these results may indicate that the first elements of mental experience emerged between amphibians and reptiles. (shrink)

During the first two years of human life a common neural substrate underlies the hierarchical organization of elements in the development of speech as well as the capacity to combine objects manually, including tool use. Subsequent cortical differentiation, beginning at age two, creates distinct, relatively modularized capacities for linguistic grammar and more complex combination of objects. An evolutionary homologue of the neural substrate for language production and manual action is hypothesized to have provided a foundation for the evolution of language (...) before the divergence of the hominids and the great apes. Support comes from the discovery of a Broca's area homologue and related neural circuits in contemporary primates. In addition, chimpanzees have an identical constraint on hierarchical complexity in both tool use and symbol combination. Their performance matches that of the two-year-old child who has not yet developed the neural circuits for complex grammar and complex manual combination of objects. (shrink)

Traditionally, phylogenetic relations among living and extinct species have been estimated from their morphology, particularly that of the bones and teeth. During the past two decades, molecular comparisons of DNA, RNA and proteins have increasingly influenced the taxonomy of living forms. Recently, radio‐immunoassay (RIA) has been applied to the resolution of phylogenetic disputes by testing the relationships of residual fossil proteins with those of living organisms.