Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.     

Towards a common strategy for transducing olfactory information

Olfactory receptor cells in phylogenetically diverse animals are strikingly similar, notwithstanding species-specific differences in organizational details. As we learn more about how olfactory receptor cells function, we see the first evidence that phylogenetic similarity may extend to the functional level. Conservation of form and function in phylogenetically diverse animals would suggest the presence of a fundamental strategy for detecting and discriminating odors. Emerging data on how olfactory receptor cells transduce odor information offers some insight into what this still unresolved strategy may be.     

Phylogeny for the faint of heart: a tutorial

Phylogenetic trees seem to be finding ever broader applications, and researchers from very different backgrounds are becoming interested in what they might have to say. This tutorial aims to introduce the basics of building and interpreting phylogenetic trees. It is intended for those wanting to understand better what they are looking at when they look at someone else's trees or to begin learning how to build their own. Topics covered include: how to read a tree, assembling a dataset, multiple sequence alignment (how it works and when it does not), phylogenetic methods, bootstrap analysis and long-branch artefacts, and software and resources.     

Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution

We present a parameterized definition of gene clusters that allows us to control the emphasis placed on conserved order within a cluster. Though motivated by biological rather than mathematical considerations, this parameter turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are, and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.     

Recreating ancestral proteins

Tracing the history of molecular changes using phylogenetic methods can provide powerful insights into how and why molecules work the way they do. It is now possible to recreate inferred ancestral proteins in the laboratory and study the function of these molecules. This provides a unique opportunity to study the paths and the mechanisms of functional change during molecular evolution. What insights have already emerged from such phylogenetic studies of protein evolution and function, what are the impediments to progress and what are the prospects for the future?     

Homoplasy, homology, and the perceived special status of behavior in evolution

Evolutionary biologists tend to tread cautiously when considering how behavioral data might be incorporated into phylogenetic analyses, largely because of the preconception that behavior somehow constitutes a "special" set of characters that may be inherently more prone to homoplasy or subject to different selection regimes than those that operate on the morphological or genetic traits traditionally used in phylogenetic reconstruction. In this review, we first consider how the evolution of behavior has been treated historically, paying particular attention to why phylogenetic reconstruction has often failed to include behavioral traits. We then discuss, from a theoretical perspective, what reasons there are--if any--for assuming that behavioral traits should be more prone to homoplasy than other types of traits. In doing so, we review several empirical studies that tackle this issue head-on. Finally, we examine how behavioral features have been used to good effect in phylogenetic reconstruction. Our conclusion is that there seems to be little justification on theoretical grounds for assuming that behavior is in any way "special"--either particularly labile or particularly prone to exhibit high levels of homoplasy. Additionally, in reviewing historical perceptions of behavior and their links to conceptions of homology, we conclude that there is no compelling reason why behavior cannot be homologized or therefore why it should not prove phylogenetically informative. In subsequently considering several factors related to selection that influence the likelihood of homoplasy occurring in any trait system, we also found no clear trend predicting homoplasy disproportionately in behavioral systems. In fact, where studied, the degree of homoplasy seen in behavioral traits is comparable to that seen in other trait systems. Ultimately, there appear to be no grounds for dismissing behavior a priori from the class of phylogenetically informative characters.     

From types to individuals: Hennig’s ontology and the development of phylogenetic systematics

Contemporary phylogenetic systematics was framed, in part, as a response to a resurgent idealistic morphology in the German‐speaking world in the first half of the 20th century. There were also conceptual and methodological challenges from Anglo‐American researchers who were sceptical about whether a phylogenetic approach to systematics could be made to work. This paper describes these challenges as a way of providing context for some ontological innovations made first by Walter Zimmermann and then by Willi Hennig. The principal argument of this paper is that what has become known as the individuality thesis played a much more important role in the conceptual foundations of Hennig’s version of phylogenetic systematics than has been widely appreciated. Understanding Hennig’s ontology illuminates his responses to objections to phylogenetic systematics from both sides of the Atlantic and sheds substantial light on the extinction part of the dichotomy rule. Although many have taken Hennig’s claim that parent species go extinct at speciation to be an arbitrary and biologically unrealistic rule, extinction of the parent follows directly from the way Hennig understands species and how they are individuated. © The Willi Hennig Society 2011.     

Lophotrochozoan mitochondrial genomes

Progress in both molecular techniques and phylogenetic methodshas challenged many of the interpretations of traditional taxonomy.One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships withinthis group and the inclusion of some phyla remain uncertain.While much of this progress in phylogenetic reconstruction hasbeen based on comparing single gene sequences, there are alsohigher order features of genomes, such as the relative orderof genes, that have contributed, and this seems likely to beeven more fruitful in the future. Even though tremendous progressis being made on the sequence determination of whole nucleargenomes, the dataset of choice for genome-level characters formany animals across a broad taxonomic range remains mitochondrialgenomes. We review here what is known about mitochondrial genomesof the lophotrochozoans and how comparisons of some of thesefeatures may be useful in discerning the phylogeny of this group.     

Discriminating the effects of phylogenetic hypothesis,tree resolution and clade age estimates on phylogenetic signal measurements

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.     

Integration, phylogeny, and the hominid cranial base

Basicranial features were examined in catarrhine primates and early hominids in order to demonstrate how information about morphological integration can be incorporated into phylogenetic analysis. Hypotheses purporting to explain the functional and structural relationships of basicranial characters were tested using factor analysis. Characters found to be functionally or structurally related to each other were then further examined in order to determine whether there was evidence that they were phylogenetically independent. If phylogenetic independence could not be demonstrated, then the characters were presumed to be integrated and were grouped into a complex. That complex was then treated as if it were a single character for the purposes of cladistic analysis. Factor analysis revealed that five basicranial features may be structurally related to relative brain size in hominoids. Depending on how one defines phylogenetic independence, as few as two, or as many as all of those characters might be morphologically integrated. A cladistic analysis of early hominids based on basicranial features revealed that the use of integrated complexes had a substantial effect on the phylogenetic position of Australopithecus africanus, a species whose relationships are poorly resolved. Moreover, the use of complexes also had an effect on reanalyses of certain published cladistic data sets, implying that those studies might have been biased by patterns of basicranial integration. These results demonstrate that patterns of morphological integration need to be considered carefully in all morphology-based cladistic analyses, regardless of taxon or anatomical focus. However, an important caveat is that the functional and structural hypotheses tested here predicted much higher degrees of integration than were observed. This result warns strongly that hypotheses of integration must be tested before they can be adequately employed in phylogenetic analysis. The uncritical acceptance of an untested hypothesis of integration is likely to be as disruptive to a cladistic analysis as when integration is ignored.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

Assessing spatial and environmental drivers of phylogenetic structure in Brazilian Araucaria forests

Evidence of phylogenetic conservatism in plant ecological traits has accumulated over the past few years, suggesting an interplay between the distribution of phylogenetic clades and major environmental gradients. Nonetheless, determining what environmental factors underlie the distribution of phylogenetic lineages remains a challenge because environmental factors are correlated with spatial gradients where the latter might indicate some degree of dispersal limitation in phylogenetic pools. We analyzed the phylogenetic structure of plant assemblages across the Brazilian Araucaria forests and assessed how phylogenetic structure responds to environmental and spatial gradients. We compiled data on plant occurrence in 45 plots across the Araucaria forest biome. The phylogenetic structure of the plots was characterized using phylogenetic fuzzy‐weighting followed by principal coordinates of phylogenetic structure (PCPS). We used distance‐based redundancy analysis (db‐RDA) to analyze the relationships between phylogenetic clades and environmental and spatial factors. Variation partitioning showed that the phylogenetic structure of Brazilian Araucaria forests was better explained by environment factors (altitude and annual mean temperature) than by space. Yet, spatially‐structured environmental variation explained about one‐third of total variation in the phylogenetic structure. Thus, the influence of spatial filters on the phylogenetic structure was more related to environmental gradients across the Brazilian Araucaria forest biome than to dispersal limitation of phylogenetic lineages. Furthermore, the influence of explanatory factors on the phylogenetic structure was concentrated in few nodes, the one splitting tree ferns from seed plants, and a second splitting malvids from other eurosids. Assessing the functional links between species distribution patterns and environmental gradients is not an easy task when we have to deal with large species pools. Identifying major phylogenetic gradients across an environmental and/or geographical range of interest can represent a first step towards a better understanding of general assembly processes in ecological communities.     

Porphobilinogen synthase,the first source of Heme's asymmetry

Porphobilinogen is the monopyrrole precursor of all biological tetrapyrroles. The biosynthesis of porphobilinogen involves the asymmetric condensation of two molecules of 5-aminolevulinate and is carried out by the enzyme porphobilinogen synthase (PBGS), also known as 5-aminolevulinate dehydratase. This review documents what is known about the mechanism of the PBGS-catalyzed reaction. The metal ion constitutents of PBGS are of particular interest because PBGS is a primary target for the environmental toxin lead. Mammalian PBGS contains two zinc ions at each active site. Bacterial and plant PBGS use a third metal ion, magnesium, as an allosteric activator. In addition, some bacterial and plant PBGS may use magnesium in place of one or both of the zinc ions of mammalian PBGS. These phylogenetic variations in metal ion usage are described along with a proposed rationale for the evolutionary divergence in metal ion usage. Finally, I describe what is known about the structure of PBGS, an enzyme which has as yet eluded crystal structure determination.     

A guide to phylogenetic metrics for conservation,community ecology and macroecology

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.     

Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.     

Taxonomy, slime molds, and the questions we ask

Taxonomic treatments often influence the way we both ask and attempt to answer certain biological questions. The classical taxonomy of the dictyostelid cellular slime molds (Dictyosteliales) involves a convenient set of categories that were developed independent of phylogeny. In order to test whether the characters supporting the classical taxonomy hold any phylogenetic signal, we subjected 19 described taxa belonging to two families (Acytosteliaceae and Dictyosteliaceae) and three genera (Acytostelium, Dictyostelium, and Polysphondylium) to rooted cladistic analyses using PAUP* v 4.0b4a. Neither family nor any of the three genera were found to represent monophyletic groups. These results confirm that the classical taxonomy used to delineate families and genera within these slime molds carries very little phylogenetic signal. Taxonomic character sets should be scrutinized phylogenetically in order to determine what information they provide about the relatedness of taxa within a group. Because taxonomy often drives the nature of biological inquiry, caution should be exercised when drawing conclusions regarding the evolution of developmental systems in Dictyostelium.     

Markov invariants, plethysms, and phylogenetics

We explore model-based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the Log–Det distance measure. We take as our primary tool group representation theory, and show that it provides a general framework for analyzing Markov processes on trees. From this algebraic perspective, the inherent symmetries of these processes become apparent, and focusing on plethysms, we are able to define Markov invariants and give existence proofs. We give an explicit technique for constructing the invariants, valid for any number of character states and taxa. For phylogenetic trees with three and four leaves, we demonstrate that the corresponding Markov invariants can be fruitfully exploited in applied phylogenetic studies.     

Woody plant phylogenetic diversity mediates bottom–up control of arthropod biomass in species-rich forests

Global change is predicted to cause non-random species loss in plant communities, with consequences for ecosystem functioning. However, beyond the simple effects of plant species richness, little is known about how plant diversity and its loss influence higher trophic levels, which are crucial to the functioning of many species-rich ecosystems. We analyzed to what extent woody plant phylogenetic diversity and species richness contribute to explaining the biomass and abundance of herbivorous and predatory arthropods in a species-rich forest in subtropical China. The biomass and abundance of leaf-chewing herbivores, and the biomass dispersion of herbivores within plots, increased with woody plant phylogenetic diversity. Woody plant species richness had much weaker effects on arthropods, but interacted with plant phylogenetic diversity to negatively affect the ratio of predator to herbivore biomass. Overall, our results point to a strong bottom–up control of functionally important herbivores mediated particularly by plant phylogenetic diversity, but do not support the general expectation that top–down predator effects increase with plant diversity. The observed effects appear to be driven primarily by increasing resource diversity rather than diversity-dependent primary productivity, as the latter did not affect arthropods. The strong effects of plant phylogenetic diversity and the overall weaker effects of plant species richness show that the diversity-dependence of ecosystem processes and interactions across trophic levels can depend fundamentally on non-random species associations. This has important implications for the regulation of ecosystem functions via trophic interaction pathways and for the way species loss may impact these pathways in species-rich forests.