Comparative methods as a statistical fix: the dangers of ignoring an evolutionary model

Abstract Comparative methods are widely used in ecology and evolution. The most frequently used comparative methods are based on an explicit evolutionary model. However, recent approaches have been popularized that are without an evolutionary basis or an underlying null model. Here we highlight the limitations of such techniques in comparative analyses by using simulations to compare two commonly used comparative methods with and without evolutionary basis, respectively: generalized least squares (GLS) and phylogenetic eigenvector regression (PVR). We find that GLS methods are more efficient at estimating model parameters and produce lower variance in parameter estimates, lower phylogenetic signal in residuals, and lower Type I error rates than PVR methods. These results can very likely be generalized to eigenvector methods that control for space and both space and phylogeny. We highlight that GLS methods can be adapted in numerous ways and that the variance structure used in these models can be flexibly optimized to each data set.     

Marine and terrestrial ecology: unifying concepts, revealing differences

The extent to which similar ecological processes operate on land and in the sea has been much debated, with apparently 'fundamental' differences often disappearing when appropriate comparisons are made. However, marine and terrestrial ecology have developed as largely separate intellectual endeavours, which has hampered the search for general patterns and mechanisms. Here, I argue that marine-terrestrial comparative studies can be extremely useful at uncovering mechanisms when they explicitly consider those facets of the environment that are important to a particular hypothesis. Furthermore, the binary 'marine-terrestrial' division misses many opportunities for more interesting comparisons, several of which I highlight here. Increasing the flow of concepts, hypotheses, and data between marine and terrestrial ecologists is essential to reveal those differences that really are important.     

Politics And Gastropolitics: Gender And The Power Of Food In Two African Pastoralist Societies

Male-centred aspects of political behaviour have generally remained the explanatory and interpretive focuses in analyses of the social organization of African pastoralists. While recent work on African pastoralists has shed increasing light on the lives of women, I argue that key assumptions underlying anthropological models of male dominance in these societies have been insufficiently challenged. Drawing on recent approaches in gender and social organization that highlight the mutual constitution of domestic and political domains, I examine comparative material from two well-known pastoralist societies: the Samburu of northern Kenya and the Nuer of southern Sudan. In doing so, I suggest strong linkages between male-dominated 'political spheres' and areas of domestic life in which the role of women is more significant – particularly processes of domestic food distribution. In re-examining central facets of Samburu politics – which are best known through Paul Spencer's seminal analysis of the gerontocratic aspects of Samburu political life – I suggest that the status and identities of Samburu men are in fundamental ways defined through their relationship to women as providers of food within Samburu households. Comparative material from the Nuer suggests, additionally, the strategic use of food by women in influencing male 'political spheres'. In comparing these cases, I suggest a more general model through which domestic processes of food allocation as realms of female-centred social action may be seen to play a central role in the forms and processes of pastoral 'political' life.     

From endophenotypes to evolution: social attachment, sexual fidelity and the avpr1a locus

Both medical and evolutionary genetics increasingly emphasize the importance of subtle, quantitative measures of phenotype. One such 'endophenotype,' the distribution of vasopressin 1a receptor (V1aR), is a recent focus for studies of social behavior. In animal studies, the neural distribution of V1aR has been linked to both social attachment and patterns of sexual fidelity. At a genetic level, a microsatellite in the cis-regulatory region of the avpr1a locus has been linked to variation in both brain and behavior. Both sets of data become more complex as the mechanistic and evolutionary details are examined more fully. I briefly summarize recent work from animal and human studies of avpr1a and highlight parallels between comparative and clinical approaches.     

From Carlquist’s ecological wood anatomy to Carlquist’s Law: why comparative anatomy is crucial for functional xylem biology

All students of xylem structure–function relations need to be familiar with the work of Sherwin Carlquist. He studies xylem through the lens of the comparative method, which uses the appearance of similar anatomical features under similar conditions of natural selection to infer function. “Function” in biology implies adaptation; maximally supported adaptation inferences require experimental and comparative xylem scientists to work with one another. Engaging with comparative inferences of xylem function will, more likely sooner rather than later, bring one to the work of Sherwin Carlquist. To mark his 90th birthday, I highlight just a few examples of his extraordinarily perceptive and general comparative insights. One is “Carlquist’s Law”, the pervasive tendency for vessels to be solitary when background cells are conductive. I cover his pioneering of “ecological” wood anatomy, viewing xylem variation as reflecting the effects of selection across climate and habit variation. Another is the embolism vulnerability–conduit diameter relationship, one of the most widely invoked structure–function relationships in xylem biology. I discuss the inferential richness within the notion of Carlquistian paedomorphosis, including detailed functional inferences regarding ray cell orientation. My final example comes from his very recent work offering the first satisfactory hypothesis accounting for the geographical and histological distribution of scalariform perforation plates as an adaptation, including “Carlquist’s Ratchet”, why scalariform plates are adaptive but do not re-evolve once lost. This extraordinarily rich production over six decades is filled with comparative inferences that should keep students of xylem function busy testing for decades to come.     

The roots of bioinformatics in theoretical biology

From the late 1980s onward, the term "bioinformatics" mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view) and I will argue that the original meaning of the term is re-emerging.     

The utility of zebrafish for studies of the comparative biology of motor systems

Although zebrafish are best known as a model for studies of development, there is now a growing role for the model in studies of the functional organization of the nervous system, including studies of a variety of sensory systems, central processing, and motor output. The zebrafish has much to offer for such work because of the unique combination of genetics, optical methods, and physiology it allows. Here I illustrate, using three examples, the broad range of avenues along which zebrafish can inform us about motor systems. The examples include efforts to understand the functional organization and evolution of spinal interneurons, the role of mutants in informing us about motor dysfunction and human disease, and the ability to use the special features of zebrafish to explore strategies to restore function after injury. The most important aspects of these studies are evident only when they are placed in a comparative context, so they serve to highlight the power of zebrafish in studies of the comparative biology of motor control.     

A Standard System to Study Vertebrate Embryos

Staged embryonic series are important as reference for different kinds of biological studies. I summarise problems that occur when using ‘staging tables’ of ‘model organisms’. Investigations of developmental processes in a broad scope of taxa are becoming commonplace. Beginning in the 1990s, methods were developed to quantify and analyse developmental events in a phylogenetic framework. The algorithms associated with these methods are still under development, mainly due to difficulties of using non-independent characters. Nevertheless, the principle of comparing clearly defined newly occurring morphological features in development (events) in quantifying analyses was a key innovation for comparative embryonic research. Up to date no standard was set for how to define such events in a comparative approach. As a case study I compared the external development of 23 land vertebrate species with a focus on turtles, mainly based on reference staging tables. I excluded all the characters that are only identical for a particular species or general features that were only analysed in a few species. Based on these comparisons I defined 104 developmental characters that are common either for all vertebrates (61 characters), gnathostomes (26), tetrapods (3), amniotes (7), or only for sauropsids (7). Characters concern the neural tube, somite, ear, eye, limb, maxillary and mandibular process, pharyngeal arch, eyelid or carapace development. I present an illustrated guide listing all the defined events. This guide can be used for describing developmental series of any vertebrate species or for documenting specimen variability of a particular species. The guide incorporates drawings and photographs as well as consideration of species identifying developmental features such as colouration. The simple character-code of the guide is extendable to further characters pertaining to external and internal morphological, physiological, genetic or molecular development, and also for other vertebrate groups not examined here, such as Chondrichthyes or Actinopterygii. An online database to type in developmental events for different stages and species could be a basis for further studies in comparative embryology. By documenting developmental events with the standard code, sequence heterochrony studies (i.e. Parsimov) and studies on variability can use this broad comparative data set.     

Bird speech perception and vocal production: a comparison with humans

Research into speech perception by nonhuman animals can be crucially informative in assessing whether specific perceptual phenomena in humans have evolved to decode speech, or reflect more general traits. Birds share with humans not only the capacity to use complex vocalizations for communication but also many characteristics of its underlying developmental and mechanistic processes; thus, birds are a particularly interesting group for comparative study. This review first discusses commonalities between birds and humans in perception of speech sounds. Several psychoacoustic studies have shown striking parallels in seemingly speech-specific perceptual phenomena, such as categorical perception of voice-onset-time variation, categorization of consonants that lack phonetic invariance, and compensation for coarticulation. Such findings are often regarded as evidence for the idea that the objects of human speech perception are auditory or acoustic events rather than articulations. Next, I highlight recent research on the production side of avian communication that has revealed the existence of vocal tract filtering and articulation in bird species-specific vocalization, which has traditionally been considered a hallmark of human speech production. Together, findings in birds show that many of characteristics of human speech perception are not uniquely human but also that a comparative approach to the question of what are the objects of perception--articulatory or auditory events--requires careful consideration of species-specific vocal production mechanisms.     

Atomistic molecular simulations of protein folding

Theory and experiment have provided answers to many of the fundamental questions of protein folding; a remaining challenge is an accurate, high-resolution picture of folding mechanism. Atomistic molecular simulations with explicit solvent are the most promising method for providing this information, by accounting more directly for the physical interactions that stabilize proteins. Although simulations of folding with such force fields are extremely challenging, they have become feasible as a result of recent advances in computational power, accuracy of the energy functions or 'force fields', and methods for improving sampling of folding events. I review the recent progress in these areas, and highlight future challenges and questions that we may hope to address with these methods. I also attempt to place atomistic models into the context of the energy landscape view of protein folding, and coarse-grained simulations.     

Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

Unresolved questions in genitalia coevolution: bridging taxonomy,speciation, and developmental genetics

Systematists and geneticists study biological diversity, but they use different approaches that rarely intersect. A very common pattern that is of interest for both researchers is the rapid evolution of genitalia, a trait of significant taxonomic utility in several sexually reproducing animal clades. The idea that both male and female genitalia are species-specific and play a role in reproductive isolation has long been controversial but has recently gained a renewed interest by speciation and developmental geneticists. Here, I highlight six unresolved questions in genitalia coevolution and I argue that systematists, with their well training in comparative morphology, usage of large and geographically diverse collections, and ability to apply molecular genetics techniques, can make important contributions. Such an extension of systematics into the speciation and developmental genetics realms is a promising opportunity to expand “integrative taxonomy” comparisons between DNA and morphology into more explanatory relationships between the two sources of taxonomic data.     

Modeling cellular machinery through biological network comparison

Molecular networks represent the backbone of molecular activity within the cell. Recent studies have taken a comparative approach toward interpreting these networks, contrasting networks of different species and molecular types, and under varying conditions. In this review, we survey the field of comparative biological network analysis and describe its applications to elucidate cellular machinery and to predict protein function and interaction. We highlight the open problems in the field as well as propose some initial mathematical formulations for addressing them. Many of the methodological and conceptual advances that were important for sequence comparison will likely also be important at the network level, including improved search algorithms, techniques for multiple alignment, evolutionary models for similarity scoring and better integration with public databases.     

Missing data imputation and haplotype phase inference for genome-wide association studies

Imputation of missing data and the use of haplotype-based association tests can improve the power of genome-wide association studies (GWAS). In this article, I review methods for haplotype inference and missing data imputation, and discuss their application to GWAS. I discuss common features of the best algorithms for haplotype phase inference and missing data imputation in large-scale data sets, as well as some important differences between classes of methods, and highlight the methods that provide the highest accuracy and fastest computational performance.     

Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners

Recent advances in high-throughput experimental methods for the identification of protein interactions have resulted in a large amount of diverse data that are somewhat incomplete and contradictory. As valuable as they are, such experimental approaches studying protein interactomes have certain limitations that can be complemented by the computational methods for predicting protein interactions. In this review we describe different approaches to predict protein interaction partners as well as highlight recent achievements in the prediction of specific domains mediating protein-protein interactions. We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them.     

Interpreting Chromosomal Rearrangements in the Context of 3-Dimentional Genome Organization: A Practical Guide for Medical Genetics

In this exciting era of “next-gen cytogenetics”, the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization. In this article, we describe the main features of 3-dimentional genome organization, emphasizing their role in normal and pathological development. We highlight some tips to help physicians estimating the impact of chromosomal rearrangements on the patient phenotype. A separate section describes available tools that can be used to visualize and analyze human genome architecture.     

An Eliminativist Approach to Vulnerability

The concept of vulnerability has been subject to numerous different interpretations but accounts are still beset with significant problems as to their adequacy, such as their contentious application or the lack of genuine explanatory role for the concept. The constant failure to provide a compelling conceptual analysis and satisfactory definition leaves the concept open to an eliminativist move whereby we can question whether we need the concept at all. I highlight problems with various kinds of approach and explain why a satisfactory account of vulnerability is unlikely ever to be offered if we wish the concept to play a genuinely explanatory role in bioethical contexts. I outline why an eliminativist position should be taken with regard to this concept in light of these concerns but mitigate some of the severity of this position by arguing that we can still make sense of retaining our widespread use of the term by viewing it as nothing more than a useful pragmatic linguistic device that acts as a marker to draw attention to certain kinds of issue. These issues will be entirely governed by other, better understood ethical concepts and theories.     

Is ‘Best Proven’ A Useless Criterion?

In this article I examine some proposals for modification of ethical documents regulating research, particularly, the problems that introducing certain economic clauses may pose. I evaluate suggestions that reject the notion of providing the 'best proven diagnostic and therapeutic method' in favor of 'the highest attainable therapeutic method' or 'the proven effective prophylactic, diagnostic and therapeutic methods'. I analyze the plausibility and problems of introducing a double standard and the consequences it may have in developing countries. Finally I highlight the impact these changes may imply for these countries.     

Controlling for non-independence in comparative analysis of patterns across populations within species

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.