Phylogeny, ecology, and the coupling of comparative and experimental approaches

Recent progress in the development of phylogenetic methods and access to molecular phylogenies has made comparative biology more popular than ever before. However, determining cause and effect in phylogenetic comparative studies is inherently difficult without experimentation and evolutionary replication. Here, we provide a roadmap for linking comparative phylogenetic patterns with ecological experiments to test causal hypotheses across ecological and evolutionary scales. As examples, we consider five cornerstones of ecological and evolutionary research: tests of adaptation, tradeoffs and synergisms among traits, coevolution due to species interactions, trait influences on lineage diversification, and community assembly and composition. Although several scenarios can result in a lack of concordance between historical patterns and contemporary experiments, we argue that the coupling of phylogenetic and experimental methods is an increasingly revealing approach to hypothesis testing in evolutionary ecology.     

Realism in systematics through biogeographical consilience

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionary processes, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a defined criterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historical series of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree of truthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize the biological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption that robust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa. © The Willi Hennig Society 2011.     

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.     

Phylogenetic frameworks: towards a firmer foundation for the comparative approach

The growing interest in using phylogenies to test evolutionary hypotheses has focused attention on the need for robust estimates of phylogenetic history. Whether specific branching structures are correct summaries of evolutionary history can be estimated only through the examination of congruence of many sets of characters. After consideration of practical and philosophical aspects of congruence, I conclude that taxonomic congruence (analysis of congruence of topologies produced from independent datasets) is preferable to character congruence (analysis of congruence between individual characters) for estimating accuracy of phylogenetic hypotheses. Existing methods for examining taxonomic congruence are discussed and the combinable components approach, when preceded by application of rigorous statistical manipulations (e.g. jackknifing or bootstrapping), found most appropriate. Implementation of the method of combinable components is described, and is demonstrated using published data for Menidia and Rana. The robust branching structure resulting from this analysis (a phylogenetic framework) contains those nodes (phylogenetic hypotheses) that are strongly supported by at least one dataset and are consistent with all others. This approach is the most appropriate/conservative for testing hypotheses about evolutionary history.     

Historical biology and the problem of design

Organisms are historical entities in that their past history plays an important role in shaping the properties they exhibit today. While this fact is widely acknowledged, little attempt has been made to develop a testable approach to the analysis of the historical factor in evolutionary morphology. The analysis of extrinsic environmental factors may reveal the limits imposed by the environment on biological design, but the intrinsic phylogenetic component of design may severely constrain the directions of structural modification that can occur. The importance of history can be assessed with (1) a phylogenetic hypothesis of genealogical relationship, (2) the use of emergent structural or functional attributes with general properties, and (3) the testing of historical hypotheses by the comparison of general properties between monophyletic lineages. The synthesis of a structural/phylogenetic approach to historical morphology with the analysis of extrinsic limits to form may provide the level of resolution needed to generate testable mechanistic hypotheses regarding the distribution of extant organismal forms in the hyperspace of possible morphologies.     

The evolution of parental care and egg size: a comparative analysis in frogs

The evolution of parental care and egg size has attracted considerable attention and theoretical debate. Several different hypotheses have been proposed concerning the trajectories of parental care and egg size evolution and the order of specific evolutionary transitions. Few comparative studies have investigated the predictions of these hypotheses. Here, we investigate the evolutionary association between parental care and egg size in frogs in a phylogenetic context. Data on egg size and presence or absence of parental care in various species of frogs was gathered from the scientific literature. As a basis for our comparative analyses, we developed a phylogenetic supertree, by combining the results of multiple phylogenetic analyses in the literature using matrix representation parsimony. Using phylogenetic pairwise comparisons we demonstrated a significant association between the evolution of parental care and large egg size. We then used recently developed maximum likelihood methods to infer the evolutionary order of specific transitions. This analysis revealed that the evolution of large egg size typically precedes the evolution of parental care, rather than the reverse. We discuss the relevance of our results to previous hypotheses concerning the evolution of parental care and egg size.     

Intercontinental community convergence of ecology and morphology in desert lizards

Evolutionary ecologists have long debated the extent to which communities in similar environments but different geographic regions exhibit convergence. On the one hand, if species' adaptations and community structure are determined by environmental features, convergence would be expected. However, if historical contingencies have long-lasting effects convergence would be unlikely. Most studies to date have emphasized the differences between communities in similar environments and little quantitative evidence for convergence exists. The application of comparative phylogenetic methods to ecological studies provides an opportunity to further investigate hypotheses of convergence. We compared the evolutionary patterns of structural ecology and morphology of 42 species of iguanian lizards from deserts of Australia and North America. Using a comparative approach, we found that evolutionary convergence of ecology and morphology occurs both in overall, community-wide patterns and in terms of pairs of highly similar intercontinental pairs of species. This result indicates that in these desert lizards, deterministic adaptive evolution shapes community patterns and overrides the historical contingencies unique to particular lineages.     

Learning from history: morphology's challenges in Germany ca. 1900

A century ago, Carl Gegenbaur's program of vertebrate evolutionary morphology faced its greatest challenges. The controversy over the evolutionary origin of the vertebrate paired limbs between 1875 and 1906 illustrates the failure of the traditional methods of comparative anatomy and embryology (supported by Haeckel's biogenetic law) to choose between different phylogenetic hypotheses. The controversy over morphology's status as science intensified at the turn of the twentieth century, when the legitimacy of historical explanation itself as a mode of scientific understanding came under fire. Gegenbaur's intellectual grandson, Hermann Braus, sought to defend the legitimacy of phylogenetic reconstruction while updating it to include experimental and causal-analytical approaches, but was unable to sustain a viable synthetic research program. The article concludes with reflections on approaches to the past used by historians and evolutionary morphologists.     

Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.     

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae)

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.     

Reconstructing shifts in diversification rates on phylogenetic trees

Few issues in evolutionary biology have received as much attention over the years or have generated as much controversy as those involving evolutionary rates. One unresolved issue is whether or not shifts in speclation and/or extinction rates are closely tied to the origin of 'key' innovations in evolution. This discussion has long been dominated by 'time-based' methods using data from the fossil record. Recently, however, attention has shifted to 'tree-based' methods, in which time, if It plays any role at all, is incorporated secondarily, usually based on molecular data. Tests of hypotheses about key innovations do require Information about phylogenetic relationships, and some of these tests can be implemented without any information about time. However, every effort should be made to obtain information about time, which greatly increases the power of such tests.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Simulation of Genomes: A Review

There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are increasing in size, with genome-wide data becoming a common place in many empirical studies. As far as more information is available, it becomes clear that simplest hypotheses are not consistent with data. Simulations will provide the key tool to contrast complex hypotheses on real data by generating simulated data under the hypothetical historical and evolutionary conditions that we want to contrast. Undoubtedly, developing tools for simulating large sequences that at the same time allow simulate natural selection, recombination and complex demography patterns will be of great interest in order to better understanding the trace left on the DNA by different interacting evolutionary forces. Simulation tools will be also essential to evaluate the sampling properties of any statistics used on genome-wide association studies and to compare performance of methods applied at genome-wide scales. Several recent simulation tools have been developed. Here, we review some of the currently existing simulators which allow for efficient simulation of large sequences on complex evolutionary scenarios. In addition, we will point out future directions in this field which are already a key part of the current research in evolutionary biology and it seems that it will be a primary tool in the future research of genome and post-genomic biology.     

Understanding phylogenetic incongruence: lessons from phyllostomid bats

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar‐feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species‐rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar‐feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well‐studied organisms such as phyllostomid bats.     

Application of phylogenetic networks in evolutionary studies

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.     

phylin: an r package for phylogeographic interpolation

phylin is a package for the r programming environment which offers different methods to spatially interpolate genetic information from phylogeographic data. These interpolations can be used to predict the spatial occurrence of different lineages within a phylogeny using a modified method of kriging, which allows the usage of a genetic distance matrix to derive a model of spatial dependence. phylin improves the available methods to generate interpolated surfaces from a phylogenetic trees by assessing the autocorrelation structure of the genetic information, interpolating the genetic data based on a statistical model, estimating the uncertainty of the predictions and identifying lineage occurrence and contact zones probability without projection of pairwise genetic distances into mid‐points between sample locations. The package also includes methods to plot interpolation surfaces and provide summary tables from the generated data and models. We provide an example of the usefulness of this tool by inferring the spatial occurrence of distinct historical evolutionary lineages of the Lataste's viper (Vipera latastei Boscá, 1878) in the Iberian Peninsula and identifying potential contact areas. The maps of phylogenetic patterns obtained with these methods provide a spatial context to test hypotheses related to processes underlying the geographic distribution of genetic diversity and to inform conservation planning.     

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.     

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.     

A METHOD FOR ASSESSING PHYLOGENETIC LEAST SQUARES MODELS FOR SHAPE AND OTHER HIGH‐DIMENSIONAL MULTIVARIATE DATA

Studies of evolutionary correlations commonly use phylogenetic regression (i.e., independent contrasts and phylogenetic generalized least squares) to assess trait covariation in a phylogenetic context. However, while this approach is appropriate for evaluating trends in one or a few traits, it is incapable of assessing patterns in highly multivariate data, as the large number of variables relative to sample size prohibits parametric test statistics from being computed. This poses serious limitations for comparative biologists, who must either simplify how they quantify phenotypic traits, or alter the biological hypotheses they wish to examine. In this article, I propose a new statistical procedure for performing ANOVA and regression models in a phylogenetic context that can accommodate high‐dimensional datasets. The approach is derived from the statistical equivalency between parametric methods using covariance matrices and methods based on distance matrices. Using simulations under Brownian motion, I show that the method displays appropriate Type I error rates and statistical power, whereas standard parametric procedures have decreasing power as data dimensionality increases. As such, the new procedure provides a useful means of assessing trait covariation across a set of taxa related by a phylogeny, enabling macroevolutionary biologists to test hypotheses of adaptation, and phenotypic change in high‐dimensional datasets.     

Revising the Bantu tree

Phylogenetic methods offer a promising advance for the historical study of language and cultural relationships. Applications to date, however, have been hampered by traditional approaches dependent on unfalsifiable authority statements: in this regard, historical linguistics remains in a similar position to evolutionary biology prior to the cladistic revolution. Influential phylogenetic studies of Bantu languages over the last two decades, which provide the foundation for multiple analyses of Bantu sociocultural histories, are a major case in point. Comparative analyses of basic lexica, instead of directly treating written words, use only numerical symbols that express non-replicable authority opinion about underlying relationships. Building on a previous study of Uto-Aztecan, here we analyse Bantu language relationships with methods deriving from DNA sequence optimization algorithms, treating basic vocabulary as sequences of sounds. This yields finer-grained results that indicate major revisions to the Bantu tree, and enables more robust inferences about the history of Bantu language expansion and/or migration throughout sub-Saharan Africa. “Early-split” versus “late-split” hypotheses for East and West Bantu are tested, and overall results are compared to trees based on numerical reductions of vocabulary data. Reconstruction of language histories is more empirically based and robust than with previous methods.