Proteins and molecular palaeontology.

Protein taxonomy has existed as a concept at least since 1958, but despite the efforts of the past 30 years, comparative studies of protein sequence, structure and distribution have not revolutionized any areas of systematics. The most interesting results of single gene phylogenies have been the anomalies, such as insulin in hystricomorphs or cytochrome c in the rattlesnake. It is likely that protein sequence information can be obtained in sufficient quality and quantity from ancient material as to change this finding? The paper will assess possibilities and the likely limitations of chemical studies of ancient protein material.     

Principles of biological comparison

The problems of comparative analyses in biology have been discussed, showing that a single comparative method does not exist. Several principles of comparison are elucidated, which include that comparisons do not have to possess a phylogenetic basis, can be horizontal or vertical, and can be genetic or nongenetic. Biological comparisons can be grouped roughly into historical and nonhistorical ones. Historical comparisons depend on the details of evolutionary theory, and include: (a) comparisons on which phylogenies and classifications are based; and (b) comparative studies using these phylogenies and classifications. Nonhistorical comparisons require pertinent nomological relationships between two or more variables, and include: (a) comparisons between variables used to elucidate these law-like relationships; and (b) comparisons in which unknown properties of one variable are deduced from the known properties of other variables - extrapolations made in biology.     

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.     

How reticulated are species?

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.     

Cats, "rats," and bats: the comparative biology of aging in the 21st century

Laboratory models have suggested a link between metabolism and life span in vertebrates, and it is well known that the evolution of specific life histories can be driven by metabolic factors. However, little is known regarding how the adoption of specific life-history strategies can shape aging and life span in populations facing different energetic demands from either a theoretical or a mechanistic viewpoint but significant insight can be gained by using a comparative approach. Comparative biology plays several roles in our understanding of the virtually ubiquitous phenomenon of aging in animals. First, it provides a critical evaluation of broad hypotheses concerning the evolutionary forces underlying the modulation of aging rate. Second, it suggests mechanistic hypotheses about processes of aging. Third, it illuminates particularly informative species because of their exceptionally slow or rapid aging rates to be interrogated about potentially novel mechanisms of aging. Although comparative biology has played a significant role in research on aging for more than a century, the new comparative biology of aging is poised to dwarf those earlier contributions, because: (1) new cellular and molecular techniques for investigating novel species are in place and more are being continually generated, (2) molecular systematics has resolved the phylogenetic relationships among a wide range of species, which allow for the implementation of analytic tools specialized for comparative biology, and (3) in addition to facilitating the construction of accurate phylogenies, the dramatic acceleration in DNA-sequencing technology is providing us with new tools for a comparative genomic approach to understanding aging.     

Epilogue – one hundred years of nemertean research: Bürger (1895) to the present

The past one hundred years of research on nemerteansis reviewed. Scientific methodology and philosophyhave advanced considerably during this period, yetnemerteans remain one of the least well known ofinvertebrate groups; nemerteans are not just membersof a minor phylum, they constitute a neglected yethighly successful assemblage of animals. Despite manyworkers in the last hundred years having madesignificant contributions to our knowledge about thisphylum of worms, many aspects of their biology arestill virtually, if not totally, unknown, and theenormous advances in many areas of scientificknowledge have not been paralleled by comparable gainsin our understanding of nemerteans.     

Perspective: the origin of flowering plants and their reproductive biology--a tale of two phylogenies

Recently, two areas of plant phylogeny have developed in ways that could not have been anticipated, even a few years ago. Among extant seed plants, new phylogenetic hypotheses suggest that Gnetales, a group of nonflowering seed plants widely hypothesized to be the closest extant relatives of angiosperms, may be less closely related to angiosperms than was believed. In addition, recent phylogenetic analyses of angiosperms have, for the first time, clearly identified the earliest lineages of flowering plants: Amborella, Nymphaeales, and a clade that includes Illiciales/ Trimeniaceae/Austrobaileyaceae. Together, the new seed plant and angiosperm phylogenetic hypotheses have major implications for interpretation of homology and character evolution associated with the origin and early history of flowering plants. As an example of the complex and often unpredictable interplay of phylogenetic and comparative biology, we analyze the evolution of double fertilization, a process that forms a diploid embryo and a triploid endosperm, the embryo-nourishing tissue unique to flowering plants. We demonstrate how the new phylogenetic hypotheses for seed plants and angiosperms can significantly alter previous interpretations of evolutionary homology and firmly entrenched assumptions about what is synapomorphic of flowering plants. In the case of endosperm, a solution to the century-old question of its potential homology with an embryo or a female gametophyte (the haploid egg-producing generation within the life cycle of a seed plant) remains complex and elusive. Too little is known of the comparative reproductive biology of extant nonflowering seed plants (Gnetales, conifers, cycads, and Ginkgo) to analyze definitively the potential homology of endosperm with antecedent structures. Remarkably, the new angiosperm phylogenies reveal that a second fertilization event to yield a biparental endosperm, long assumed to be an important synapomorphy of flowering plants, cannot be conclusively resolved as ancestral for flowering plants. Although substantive progress has been made in the analysis of phylogenetic relationships of seed plants and angiosperms, these efforts have not been matched by comparable levels of activity in comparative biology. The consequence of inadequate comparative biological information in an age of phylogenetic biology is a severe limitation on the potential to reconstruct key evolutionary historical events.     

The Cell Biology of the Endocytic System from an Evolutionary Perspective

Evolutionary cell biology can afford an interdisciplinary comparative view that gives insights into both the functioning of modern cells and the origins of cellular systems, including the endocytic organelles. Here, we explore several recent evolutionary cell biology studies, highlighting investigations into the origin and diversity of endocytic systems in eukaryotes. Beginning with a brief overview of the eukaryote tree of life, we show how understanding the endocytic machinery in a select, but diverse, array of organisms provides insights into endocytic system origins and predicts the likely configuration in the last eukaryotic common ancestor (LECA). Next, we consider three examples in which a comparative approach yielded insight into the function of modern cellular systems. First, using ESCRT-0 as an example, we show how comparative cell biology can discover both lineage-specific novelties (ESCRT-0) as well as previously ignored ancient proteins (Tom1), likely of both evolutionary and functional importance. Second, we highlight the power of comparative cell biology for discovery of previously ignored but potentially ancient complexes (AP5). Finally, using examples from ciliates and trypanosomes, we show that not all organisms possess canonical endocytic pathways, but instead likely evolved lineage-specific mechanisms. Drawing from these case studies, we conclude that a comparative approach is a powerful strategy for advancing knowledge about the general mechanisms and functions of endocytic systems.The endomembrane system mediates transport of lipids, proteins, and other molecules to the various locations in the eukaryotic cell. It also underlies the interactions with the extracellular environment, presenting material at the cell surface as well as secreting and internalizing material. In modern cells, these latter aspects are important for signal transduction, surface remodeling, and nutrient acquisition. Just as these abilities are crucial to modern cells, they were likely equally important for the very first eukaryotes as they underwent speciation from prokaryotic-like ancestors via niche competition in the ancient world (Cavalier-Smith 2002). Understanding the events and biological processes involved in the evolution of the membrane-trafficking system in general, and the endocytic system in particular, gives us insights into landmark events in our cellular past.Evolutionary insight about cellular phenomenon is derived from two basic types of comparative study: from molecular cell biological analyses of increasingly tractable model organisms across the diversity of eukaryotes, and by computational analyses of genomic information (i.e., the genes encoding the membrane-trafficking machinery). Whereas the information gathered from taking this comparative, or evolutionary cell biology, approach (Brodsky et al. 2012) is valuable for evolutionary content, these same analyses are potentially highly valuable in understanding basic cell biology, a benefit that is perhaps less obvious and hence less appreciated. In this article, we frame what has been learned about the evolution of the endocytic system, in the dual context of what it tells us about ancient cells together with what it can tell us about modern ones. We begin with a brief introduction to eukaryotic diversity and the evolution of the membrane-trafficking system. We then delve into the evolution of specific endocytic factors to illustrate the ways in which cell biologists of all stripes can benefit from the emerging field of evolutionary cell biology.     

Euclidean nature of phylogenetic distance matrices

Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical constraint and aim at partitioning trait values into a phylogenetic component (phylogenetic inertia) and one or multiple specific components related to adaptive evolution. The way phylogenetic information is incorporated into the PCMs depends on the method used. For the first group of methods, phylogenies are converted into variance-covariance matrices of traits following a given model of evolution such as Brownian motion (BM). For the second group of methods, phylogenies are converted into distance matrices that are subsequently transformed into Euclidean distances to perform principal coordinate analyses. Here, we show that simply taking the elementwise square root of a distance matrix extracted from a phylogenetic tree ensures having a Euclidean distance matrix. This is true for any type of distances between species (patristic or nodal) and also for trees harboring multifurcating nodes. Moreover, we illustrate that this simple transformation using the square root imposes less geometric distortion than more complex transformations classically used in the literature such as the Cailliez method. Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance-covariance matrix of a trait following a BM model, or related models of trait evolution, can be established. In that way, we build a bridge between the two groups of statistical methods widely used in comparative analysis. These results should be of great interest for ecologists and evolutionary biologists performing statistical analyses incorporating phylogenies.     

Predicting the past distribution of species climatic niches

Predicting past distributions of species climatic niches, hindcasting, by using climate envelope models (CEMs) is emerging as an exciting research area. CEMs are used to examine veiled evolutionary questions about extinctions, locations of past refugia and migration pathways, or to propose hypotheses concerning the past population structure of species in phylogeographical studies. CEMs are sensitive to theoretical assumptions, to model classes and to projections in non-analogous climates, among other issues. Studies hindcasting the climatic niches of species often make reference to these limitations. However, to obtain strong scientific inferences, we must not only be aware of these potential limitations but we must also overcome them. Here, I review the literature on hindcasting CEMs. I discuss the theoretical assumptions behind niche modelling, i.e. the stability of climatic niches through time and the equilibrium of species with climate. I also summarize a set of 'recommended practices' to improve hindcasting. The studies reviewed: (1) rarely test the theoretical assumptions behind niche modelling such as the stability of species climatic niches through time and the equilibrium of species with climate; (2) they only use one model class (72% of the studies) and one palaeoclimatic reconstruction (62.5%) to calibrate their models; (3) they do not check for the occurrence of non-analogous climates (97%); and (4) they do not use independent data to validate the models (72%). Ignoring the theoretical assumptions behind niche modelling and using inadequate methods for hindcasting CEMs may well entail a cascade of errors and naïve ecological and evolutionary inferences. We should also push integrative research lines linking macroecology, physiology, population biology, palaeontology, evolutionary biology and CEMs for a better understanding of niche dynamics across space and time.     

PHYLOGENIES WITHOUT FOSSILS

Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.     

The 10kTrees website: A new online resource for primate phylogeny

The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities. 1 - 4 The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex, 5 , 6 that primate territoriality favors a longer day range relative to home range size, 7 and that sperm competition can account for the evolution of primate testes size. 8 , 9 Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet. 10 - 13 Recent advances in comparative methods require phylogenetic information, 2 , 14 - 16 but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.     

EXPLOSIVE RADIATION OR CRYPTIC MASS EXTINCTION? INTERPRETING SIGNATURES IN MOLECULAR PHYLOGENIES

How biodiversity is generated and maintained underlies many major questions in evolutionary biology, particularly relating to the tempo and pattern of diversification through time. Molecular phylogenies and new analytical methods provide additional tools to help interpret evolutionary processes. Evolutionary rates in lineages sometimes appear punctuated, and such "explosive" radiations are commonly interpreted as adaptive, leading to causative key innovations being sought. Here we argue that an alternative process might explain apparently rapid radiations ("broom-and-handle" or "stemmy" patterns seen in many phylogenies) with no need to invoke dramatic increase in the rate of diversification. We use simulations to show that mass extinction events can produce the same phylogenetic pattern as that currently being interpreted as due to an adaptive radiation. By comparing simulated and empirical phylogenies of Australian and southern African legumes, we find evidence for coincident mass extinctions in multiple lineages that could have resulted from global climate change at the end of the Eocene.     

Teleology and its constitutive role for biology as the science of organized systems in nature

'Nothing in biology makes sense, except in the light of teleology'. This could be the first sentence in a textbook about the methodology of biology. The fundamental concepts in biology, e.g. 'organism' and 'ecosystem', are only intelligible given a teleological framework. Since early modern times, teleology has often been considered methodologically unscientific. With the acceptance of evolutionary theory, one popular strategy for accommodating teleological reasoning was to explain it by reference to selection in the past: functions were reconstructed as 'selected effects'. But the theory of evolution obviously presupposes the existence of organisms as organized and regulated, i.e. functional systems. Therefore, evolutionary theory cannot provide the foundation for teleology. The underlying reason for the central methodological role of teleology in biology is not its potential to offer particular forms of (evolutionary) explanations for the presence of parts, but rather an ontological one: organisms and other basic biological entities do not exist as physical bodies do, as amounts of matter with a definite form. Rather, they are dynamic systems in stable equilibrium; despite changes of their matter and form (in metabolism and metamorphosis) they maintain their identity. What remains constant in these kinds of systems is their 'organization', i.e. the causal pattern of interdependence of parts with certain effects of each part being relevant for the working of the system. Teleological analysis consists in the identification of these system-relevant effects and at the same time of the system as a whole. Therefore, the identity of biological systems cannot be specified without teleological reasoning.     

How the leopard got its spots: a phylogenetic view of the evolution of felid coat patterns

The current theory of felid coat pattern evolution proposes that the primitive pattern is one of relatively large spots that break down into smaller spots (here denoted flecks) and rosettes while at the same time leading to various striped patterns as sidelines. We have coded the coat patterns of felids into uniform, flecks, rosettes, vertical stripes, small blotches and blotches and show by mapping these character states onto phylogenies of the family that the current theory is flawed. Instead, the primitive pattern appears to be flecks and it is from this type that nearly all other types have developed. The robustness of this hypothesis is shown by the fact that it remains unchanged regardless of which of several quite different, competing phylogenies of the family is used. The pattern of transformations reconstructed is not predicted by current theories of pattern formation and we suggest that modellers pay closer attention to the phylogenetic histories of the features that they model.     

Essential genes on metabolic maps

Within the past five years genome-scale gene essentiality data sets have been published for ten diverse bacterial species. These data are a rich source of information about cellular networks that we are only beginning to explore. The analysis of these data, very heterogeneous in nature, is a challenging task. Even the definition of 'essential genes' in various genome-scale studies varies from genes 'absolutely required for survival' to those 'strongly contributing to fitness' and robust competitive growth. A comparative analysis of gene essentiality across multiple organisms based on projection of experimentally observed essential genes to functional roles in a collection of metabolic pathways and subsystems is emerging as a powerful tool of systems biology.     

Phylogeny affects estimation of metabolic scaling in mammals

Abstract.— The relationship between body size and metabolic rate is a crucial issue in organismal biology and evolution. There has been considerable debate over whether the scaling exponent of the relationship is 0.75 (Kleiber's Law) or 0.67. Here we show that determination of this exponent for mammals depends on both the evolutionary tree and the regression model used in the comparative analysis. For example, more recent molecular-based phylogenies tend to support a 0.67 exponent, whereas older phylogenies, mostly based on morphological data, suggest a 0.75 exponent. However, molecular phylogenies yield more variable results than morphological phylogenies and thus are not currently helping to resolve the issue.     

The Use (and Misuse) of Phylogenetic Trees in Comparative Behavioral Analyses

Phylogenetic comparative methods play a critical role in our understanding of the adaptive origin of primate behaviors. To incorporate evolutionary history directly into comparative behavioral research, behavioral ecologists rely on strong, well-resolved phylogenetic trees. Phylogenies provide the framework on which behaviors can be compared and homologies can be distinguished from similarities due to convergent or parallel evolution. Phylogenetic reconstructions are also of critical importance when inferring the ancestral state of behavioral patterns and when suggesting the evolutionary changes that behavior has undergone. Improvements in genome sequencing technologies have increased the amount of data available to researchers. Recently, several primate phylogenetic studies have used multiple loci to produce robust phylogenetic trees that include hundreds of primate species. These trees are now commonly used in comparative analyses and there is a perception that we have a complete picture of the primate tree. But how confident can we be in those phylogenies? And how reliable are comparative analyses based on such trees? Herein, we argue that even recent molecular phylogenies should be treated cautiously because they rely on many assumptions and have many shortcomings. Most phylogenetic studies do not model gene tree diversity and can produce misleading results, such as strong support for an incorrect species tree, especially in the case of rapid and recent radiations. We discuss implications that incorrect phylogenies can have for reconstructing the evolution of primate behaviors and we urge primatologists to be aware of the current limitations of phylogenetic reconstructions when applying phylogenetic comparative methods.     

Studies on the molecular evolution of the Crocodylia: footprints in the sands of time

A reasonably large number of studies focusing on the molecular evolution of crocodilians have been completed during the past 100 years. Proteins were initially studied before DNA was known to carry the genetic information of cells and organisms, and were subsequently studied to infer changes at the DNA level. More recently, studies on the DNA itself have been completed. We have had the pleasure of taking part in or facilitating many studies conducted over the past 50 years, especially several of the earliest studies done using newly developed molecular techniques. We provide a review of the molecular genetic studies on crocodilians, summarizing the findings of these studies as well as the context in which they were undertaken. This review is a personal look at the history of molecular studies on the evolutionary biology of crocodilians. Our excuse for this focus is that our professors, our students and we have had the opportunity to be among the first to apply many new techniques to studies of crocodilians since 1950, when one of us (HCD) was a graduate student of Roland Coulson and Tom Hernandez. Although we will review much of the material in this subject area, we do not claim that it is complete. Instead, we focus our presentation on work in which we have participated or with which we are particularly familiar. We especially focus on materials relevant to the research presented at the 2(nd) International Crocodilian DNA Workshop, 7-9 November, 2001, at the San Diego Zoo. Thus, the following review also stands as a tribute to our mentors, students, and colleagues.     

Structure and function of the notochord: an essential organ for chordate development

The notochord is the defining structure of the chordates, and has essential roles in vertebrate development. It serves as a source of midline signals that pattern surrounding tissues and as a major skeletal element of the developing embryo. Genetic and embryological studies over the past decade have informed us about the development and function of the notochord. In this review, I discuss the embryonic origin, signalling roles and ultimate fate of the notochord, with an emphasis on structural aspects of notochord biology.