Recent developments in the analysis of comparative data

Comparative methods can be used to test ideas about adaptation by identifying cases of either parallel or convergent evolutionary change across taxa. Phylogenetic relationships must be known or inferred if comparative methods are to separate the cross-taxonomic covariation among traits associated with evolutionary change from that attributable to common ancestry. Only the former can be used to test ideas linking convergent or parallel evolutionary change to some aspect of the environment. The comparative methods that are currently available differ in how they manage the effects brought about by phylogenetic relationships. One method is applicable only to discrete data, and uses cladistic techniques to identify evolutionary events that depart from phylogenetic trends. Techniques for continuous variables attempt to control for phylogenetic effects in a variety of ways. One method examines the taxonomic distribution of variance to identify the taxa within which character variation is small. The method assumes that taxa with small amounts of variation are those in which little evolutionary change has occurred, and thus variation is unlikely to be independent of ancestral trends. Analyses are then concentrated among taxa that show more variation, on the assumption that greater evolutionary change in the character has taken place. Several methods estimate directly the extent to which ancestry can predict the observed variation of a character, and subtract the ancestral effect to reveal variation of phylogeny. Yet another can remove phylogenetic effects if the true phylogeny is known. One class of comparative methods controls for phylogenetic effects by searching for comparative trends within rather than across taxa. With current knowledge of phylogenies, there is a trade-off in the choice of a comparative method: those that control phylogenetic effects with greater certainty are either less applicable to real data, or they make restrictive or untestable assumptions. Those that rely on statistical patterns to infer phylogenetic effects may not control phylogeny as efficiently but are more readily applied to existing data sets.     

Molecular distance and divergence time in carnivores and primates

Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the results of empirical studies conflict and are difficult to compare because they differ widely in their choice of taxa, genetic techniques, or methods for calibrating rates of molecular evolution. We use a single methodology to analyze the relationship of molecular distance and divergence time in 86 taxa (72 carnivores and 14 primates). These taxa have divergence times of 0.01-55 Myr and provide a graded series of phylogenetic divergences such that the shape of the curve relating genetic distance and divergence time is often well defined. The techniques used to obtain genetic distance estimates include one- and two-dimensional protein electrophoresis, DNA hybridization, and microcomplement fixation. Our results suggest that estimates of molecular distance and divergence time are highly correlated. However, rates of molecular evolution are not constant; rather, in general they decline with increasing divergence time in a linear fashion. The rate of decline may differ according to technique and taxa. Moreover, in some cases the variability in evolutionary rates changes with increasing divergence time such that the accuracy of nodes in a phylogenetic tree varies predictably with time.     

Testing the relationship between morphological and molecular rates of change along phylogenies

Abstract.— Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an association between rates of morphological and molecular change estimated for "total-evidence" phylogenies, a finding that led some researchers to challenge molecular date estimates of major evolutionary radiations. Here we show that Omland's (1997) result is probably due to methodological bias, particularly phylogenetic nonindependence, rather than being indicative of an underlying evolutionary phenomenon. We apply three new methods specifically designed to overcome phylogenetic bias to 13 published phylogenetic datasets for vertebrate taxa, each of which includes both morphological characters and DNA sequence data. We find no evidence of an association between rates of molecular and morphological rates of change.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Platyhelminth systematics and the emergence of new characters

Since the inclusion of molecular data in modern phylogenetic analyses, significant progress in resolving the origins and radiation of flatworms has been made, although some key problems remain. Here I review developments in the supply and use of systematic characters that provide the basis for diagnosis and phylogeny reconstruction, that in turn have driven systematic revisions and the interpretation of broader evolutionary patterns and processes; focus is placed on the parasitic taxa. Although useful tools have been refined to the point of becoming established systematic markers of broad utility, attention to the need for denser gene and taxon sampling is addressed in the light of unresolved questions and current trends in molecular systematics, from nucleotide to genome. Tradition and the nature of available comparative information tends to dictate the choice of systematic markers, but faced with incongruent phylogenies, the emergence of new technologies and the need for rapid species diagnosis, there is a pressing need to assess and standardize our choice of tools so they are fit for purpose, available to all and used widely. I present a brief review of existing and potential sources of phylogenetic characters and discuss their likely value in the context of the systematics and diagnostics of parasitic flatworms.     

Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach

MOTIVATION: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination. RESULTS: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies.     

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.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

The pattern, timing and extent of the evolutionary radiation of anatomically modern birds (Neornithes) remains contentious: dramatically different timescales for this major event in vertebrate evolution have been recovered by the 'clock-like' modelling of molecular sequence data and from evidence extracted from the known fossil record. Because current synthesis would lead us to believe that fossil and nonfossil evidence conflict with regard to the neornithine timescale, especially at its base, it is high time that available data are reconciled to determine more exactly the evolutionary radiation of modern birds. In this review we highlight current understanding of the early fossil history of Neornithes in conjunction with available phylogenetic resolution for the major extant clades, as well as recent advancements in genetic methods that have constrained time estimates for major evolutionary divergences. Although the use of molecular approaches for timing the radiation of Neornithes is emphasized, the tenet of this review remains the fossil record of the major neornithine subdivisions and better-preserved taxa. Fossils allowing clear phylogenetic constraint of taxa are central to future work in the production of accurate molecular calibrations of the neornithine evolutionary timescale.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 141 , 153–177.     

Molecular phylogenetics and the evolution of labral spines among eastern Pacific ocenebrine gastropods

Labral spines are sharp projections of the apertural lip found in some marine gastropods that are used to penetrate hard-shelled prey. The majority of gastropod genera that contain labral spine-bearing species are found in the subfamily Ocenebrinae (Gastropoda: Muricidae). To reconstruct the evolutionary history of labral spine-bearing and labral spine-lacking gastropods in the eastern Pacific (EP) Ocean, partial sequences of two mitochondrial genes (cytochrome oxidase I and 12S rRNA) were obtained from representative taxa. Despite high nucleotide bias, a variety of phylogenetic reconstruction methods produced the same tree topology. The traditional taxonomic view that all "Nucella-like" spine-bearing taxa in the EP belong to a monophyletic "Acanthina" is rejected due to nonmonophyly of this group. The more recently recognized "Acanthinucella" is also not monophyletic, and we therefore propose the new genus Mexacanthina for two Mexican species formerly assigned to Acanthinucella. The genus Ocinebrina, which first appears in the middle Eocene, is not a stem EP ocenebrine lineage and may also not be a monophyletic clade. Tracing the evolutionary history of labral spines among extant lineages indicates that the absence of a labral spine is ancestral for all EP ocenebrines. Ancestral conditions could not be resolved unambiguously for all nodes of the phylogeny based on extant taxa. However, by jointly considering both molecular phylogenetic relationships and the phylogenetic affinities of several extinct taxa, all remaining character state transformation can be inferred unambiguously. Based on this analysis, a labral spine likely evolved independently in at least four lineages of EP ocenebrines. Although homoplasy appears to characterize labral spine evolution among ocenebrine gastropods, the structural position of a labral spine was evolutionarily altered in one lineage, indicating that different types of labral spines do not necessarily reflect convergent evolution.     

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.     

Magic bullets and golden rules: data sampling in molecular phylogenetics

Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no ‘magic bullet’ that will fit all phylogenetic problems, and no specific ‘golden rules’ have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6–10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.     

Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.     

中生代银杏类植物系统发育、分类和演化趋向

长期以来银杏类植物化石分类都依据营养叶形态为基础。由于叶形态的多型性和异源性,导致分类和系统发育解释的紊乱。根据对保存完好的繁殖器官(胚珠器官)系统发育分析结果所作的银杏目分类表明中生代除了银杏和银杏科以外,至少还存在着3．5个已灭绝的科级单元。此方案把已知其繁殖器官的成员和仅仅根据营养器官建立起来的分类位置不明的属严格地区分开来,并注明各科的限定性特征和已知成员的地质地理分布。银杏目植物自古生代起源,至早中生代以后朝着不同的方向辐射,呈现出丰富的多样性并经历了错综复杂的演化过程,其总的演化趋向是退缩：叶片扁化、蹊化和融合;胚珠器官简化,胚珠增大、数目减少,珠柄趋于消失。     

Ecological and Phylogenetic Correlates to Body Size in the Indriidae

I investigated ecological and phylogenetic correlates to body size variations in 10 taxa of extant Indriidae (Indri, Avahi, and Propithecus). I also tested for phylogenetic niche conservatism as a model for the evolution of indriid body size. Phylogenetic niche conservatism refers to the shared attributes that related taxa have acquired because they tend to have occupied similar niches during their evolutionary history. I collected species-specific data on body mass, climate, density, and chemical properties of food items from the literature. I used 2 phylogenies in independent contrasts methods to control for phylogenetic relationships (Indri and Propithecus as sister taxa vs. Indri basal taxa to all indriids). Multivariate models indicated that lemur density and resource quality are the strongest ecological correlates to indriid body size variations. Partitioning methods revealed that 52.4–67% of indriid body size variation is explained by phylogenetic niche conservation. Thus, indriid body size variations may be the result of stabilizing selection. Though it is possible to identify constraints on lower than average body size, there are few data on selection against larger than average body size in indriids. Large body size in subfossil lemurs further complicates identification of constraints on larger than average body size in extant indriids. Researchers using independent contrast methods to control for phylogeny should be aware that some ecology-phenotype relationships are best explained as the result of the synergistic effects of ecology and phylogeny.     

Parallel evolution in the hominoid trunk and forelimb

The evolutionary history of the living hominoids has remained elusive despite years of exploration and the discovery of numerous Miocene fossil ape species. Part of the difficulty can be attributed to the changing nature of our views about the course of hominoid evolution. In the 1950s and 1960s, individual Miocene taxa were commonly viewed as the direct ancestors of specific living ape species, suggesting an early divergence of the modern lineages.^1–5 However, in most cases, the Miocene forms were essentially “dental apes,” resembling extant species in dental and a few cranial features, but possessing more primitive postcranial features that suggested arboreal quadrupedalism rather than suspensory habits. With the introduction of molecular methods of phylogenetic reconstruction and the increasing use of cladistic analysis, it has become apparent that the radiation leading to the modern hominoids was somewhat more recent than had been believed, and that most of the Miocene hominoid species had little to do with the evolutionary history of the living apes. © 1998 Wiley-Liss, Inc.     

Molecular phylogenetics of representative Paramecium species

The genus Paramecium has been known to science for 250 years and contains some of the most widely studied species of ciliates. At present, the basic research object for phylogenetic studies is the genome of various paramecia. One of the most widely used markers are genes coding for various rRNA's. Comparative analyses of sequences coding rRNA were applied for resolving the systematic position of some paramecia species and also for the establishment of an accurate taxonomy of Paramecium. Paramecia were also model organisms for their systematic group in more general studies in a comparative analysis among ciliates, fungi, plants and multicellular animals, illustrating the evolutionary relationships between Archaebacteria and Eucaryota. A new, revolutionary genealogy proposed the shifting of presumptively advanced groups towards more primitive ones, and traditionally primitive forms were located closer to highly specialized taxa, but rRNA analysis did not unambiguously resolve associations within the studied groups. Because of the aforementioned concerns, the number of molecular markers used for alternative studies is growing, such as genes coding proteins from the Hsp family or histone proteins. Other promising candidate markers may be hemoglobin genes or genes coding á-tubulins. In case of comparative analyses ofnucleotide sequences, the outcome of the research usually depends upon a subjective choice of DNA. One of the directions of research in molecular phylogenetics include indirect methods that allow for an estimation of entire genomes, for example RAPD-PCR-fingerprinting.     

Molecular phylogenetics at the population/species interface in cave spiders of the southern Appalachians (Araneae:Nesticidae:Nesticus)

This paper focuses on the relationship between population genetic structure and speciation mechanisms in a monophyletic species group of Appalachian cave spiders (Nesticus). Using mtDNA sequence data gathered from 256 individuals, I analyzed patterns of genetic variation within and between populations for three pairs of closely related sister species. Each sister-pair comparison involves taxa with differing distributional and ecological attributes; if these ecological attributes are reflected in basic demographic differences, then speciation might proceed differently across these sister taxa comparisons. Both frequency-based and gene tree analyses reveal that the genetic structure of the Nesticus species studied is characterized by similar and essentially complete population subdivision, regardless of differences in general ecology. These findings contrast with results of prior genetic studies of cave-dwelling arthropods that have typically revealed variation in population structure corresponding to differences in general ecology. Species fragmentation through both extrinsic and intrinsic evolutionary forces has resulted in discrete, perhaps independent, populations within morphologically defined species. Large sequence divergence values observed between populations suggest that this independence may extend well into the past. These patterns of mtDNA genealogical structure and divergence imply that species as morphological lineages are currently more inclusive than basal evolutionary or phylogenetic units, a suggestion that has important implications for the study of speciation mechanisms.      

Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?

Taxon sampling may be critically important for phylogenetic accuracy because adding taxa can help to subdivide misleading long branches. Although the idea that added taxa can break up long branches was exemplified by a study of "incomplete" fossil taxa, the issue of taxon completeness (i.e., proportion of missing data) has been largely ignored in most subsequent discussions of taxon sampling and long-branch attraction. In this article, I use simulations to test the ability of incomplete taxa to subdivide long branches and improve phylogenetic accuracy in situations of potential long-branch attraction. The results show that for most methods and conditions examined, adding taxa that are only 50% complete may provide similar benefits to adding the same number of complete taxa (suggesting that the advantages of increased taxon sampling may be obtained with less data than previously considered). For parsimony, taxa that are less complete (5% to 25% complete) may often have limited ability to rescue analyses from long-branch attraction. In contrast, highly incomplete taxa can be surprisingly beneficial when using model-based methods. The results also suggest the importance of model-based methods in phylogenetic analyses that combine molecular and fossil data.