Garbage in, Garbage out

DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.

A supertree of Northern European macromoths

Ecological and life-history data on the Northern European macromoth (Lepidoptera: Macroheterocera) fauna is widely available and ideal for use in answering phylogeny-based research questions: for example, in comparative biology. However, phylogenetic information for such studies lags behind. Here, as a synthesis of all currently available phylogenetic information on the group, we produce a supertree of 114 Northern European macromoth genera (in four superfamilies, with Geometroidea considered separately), providing the most complete phylogenetic picture of this fauna available to date. In doing so, we assess those parts of the phylogeny that are well resolved and those that are uncertain. Furthermore, we identify those genera for which phylogenetic information is currently too poor to include in such a supertree, or entirely absent, as targets for future work. As an aid to studies involving these genera, we provide information on their likely positions within the macromoth tree. With phylogenies playing an ever more important role in the field, this supertree should be useful in informing future ecological and evolutionary studies.

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates

BACKGROUND

Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins.

RESULTS

Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules.

CONCLUSIONS

Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.

Demystifying computer science for molecular ecologists

In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Amalgamating source trees with different taxonomic levels

Supertree methods combine a collection of source trees into a single parent tree or supertree. For almost all such methods, the terminal taxa across the source trees have to be non-nested for the output supertree to make sense. Motivated by Page, the first supertree method for combining rooted source trees where the taxa can be hierarchically nested is called AncestralBuild. In addition to taxa labeling the leaves, this method allows the rooted source trees to have taxa labeling some of the interior nodes at a higher taxonomic level than their descendants (e.g., genera vs. species). However, the utility of AncestralBuild is somewhat restricted as it is mostly intended to decide if a collection of rooted source trees is compatible. If the initial collection is not compatible, then no tree is returned. To overcome this restriction, we introduce here the MultiLevelSupertree (MLS) supertree method whose input is the same as that for AncestralBuild, but which accommodates incompatibilities among rooted source trees using a MinCut-like procedure. We show that MLS has several desirable properties including the preservation of common subtrees among the source trees, the preservation of ancestral relationships whenever they are compatible, as well as running in polynomial time. Furthermore, application to a small test data set (the mammalian carnivore family Phocidae) indicates that the method correctly places nested taxa at different taxonomic levels (reflecting vertical signal), even in cases where the input trees harbor a significant level of conflict between their clades (i.e., in their horizontal signal).

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

BACKGROUND

Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.

RESULTS

In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.

CONCLUSIONS

Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

Vertebral evolution and the diversification of squamate reptiles

Taxonomic, morphological, and functional diversity are often discordant and independent components of diversity. A fundamental and largely unanswered question in evolutionary biology is why some clades diversify primarily in some of these components and not others. Dramatic variation in trunk vertebral numbers (14 to >300) among squamate reptiles coincides with different body shapes, and snake-like body shapes have evolved numerous times. However, whether increased evolutionary rates or numbers of vertebrae underlie body shape and taxonomic diversification is unknown. Using a supertree of squamates including 1375 species, and corresponding vertebral and body shape data, we show that increased rates of evolution in vertebral numbers have coincided with increased rates and disparity in body shape evolution, but not changes in rates of taxonomic diversification. We also show that the evolution of many vertebrae has not spurred or inhibited body shape or taxonomic diversification, suggesting that increased vertebral number is not a key innovation. Our findings demonstrate that lineage attributes such as the relaxation of constraints on vertebral number can facilitate the evolution of novel body shapes, but that different factors are responsible for body shape and taxonomic diversification.

What factors shape rates of phenotypic evolution? A comparative study of cranial morphology of four mammalian clades

Understanding why rates of morphological evolution vary is a major goal in evolutionary biology. Classical work suggests that body size, interspecific competition, geographic range size and specialization may all be important, and each may increase or decrease rates of evolution. Here, we investigate correlates of proportional evolutionary rates in phalangeriform possums, phyllostomid bats, platyrrhine monkeys and marmotine squirrels, using phylogenetic comparative methods. We find that the most important correlate is body size. Large species evolve the fastest in all four clades, and there is a nonlinear relationship in platyrrhines and phalangeriformes, with the slowest evolution in species of intermediate size. We also find significant increases in rate with high environmental temperature in phyllostomids, and low mass-specific metabolic rate in marmotine squirrels. The mechanisms underlying these correlations are uncertain and appear to be size specific. We conclude that there is significant variation in rates of evolution, but that its meaning is not yet clear.

The supertree tool kit

BACKGROUND

Large phylogenies are crucial for many areas of biological research. One method of creating such large phylogenies is the supertree method, but creating supertrees containing thousands of taxa, and hence providing a comprehensive phylogeny, requires hundred or even thousands of source input trees. Managing and processing these data in a systematic and error-free manner is challenging and will become even more so as supertrees contain ever increasing numbers of taxa. Protocols for processing input source phylogenies have been proposed to ensure data quality, but no robust software implementations of these protocols as yet exist.

FINDINGS

The aim of the Supertree Tool Kit (STK) is to aid in the collection, storage and processing of input source trees for use in supertree analysis. It is therefore invaluable when creating supertrees containing thousands of taxa and hundreds of source trees. The STK is a Perl module with executable scripts to carry out various steps in the processing protocols. In order to aid processing we have added meta-data, via XML, to each tree which contains information such as the bibliographic source information for the tree and how the data were derived, for instance the character data used to carry out the original analysis. These data are essential parts of previously proposed protocols.

CONCLUSIONS

The STK is a bioinformatics tool designed to make it easier to process source phylogenies for inclusion in supertree analysis from hundreds or thousands of input source trees, whilst reducing potential errors and enabling easy sharing of such datasets. It has been successfully used to create the largest known supertree to date containing over 5000 taxa from over 700 source phylogenies.

Eusociality and the success of the termites: insights from a supertree of dictyopteran families

Sociality in insects may negatively impact on species richness. We tested whether termites have experienced shifts in diversification rates through time. Supertree methods were used to synthesize family-level relationships within termites, cockroaches and mantids. A deep positive shift in diversification rate is found within termites, but not in the cockroaches from which they evolved. The shift is responsible for most of their extant species richness suggesting that eusociality is not necessarily detrimental to species richness, and may sometimes have a positive effect. Mechanistic studies of speciation and extinction in eusocial insects are advocated.

Phylogenetic analysis of sexual systems in Inuleae (Asteraceae)

From an ancestor with bisexual flowers, plants with unisexual flowers, or even unisexual individuals have evolved in different lineages of angiosperms. The Asteraceae tribe Inuleae includes hermaphroditic, monoecious, dioecious, and gynomonoecious species. Gynomonoecy, the sexual system in which female and bisexual flowers occur on the same plant, is prevalent in the Asteraceae. We inferred one large gene phylogeny (ndhF) and two supertrees to investigate whether gynomonoecy was a stage in the evolution from hermaphroditism to monoecy. We identified transitions in sexual system evolution using the stochastic character mapping method. From gynomonoecious ancestors, both hermaphroditic and monoecious descendants have evolved. Gynomonoecy was not restricted to a stage in the evolution toward monoecy because the number of transitions and the rate of change from monoecy to gynomonoecy were much higher than the opposite. We also investigated one hypothesized association among female flowers and the development of a petaloid ray as an explanation of gynomonoecy maintenance in Asteraceae. We found that peripheral female flowers and petaloid rays were phylogenetically correlated. However, empirical evidence shows that a causal relationship between these traits is not clear.

Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics

Whereas previous studies have investigated correlates of extinction risk either at global or regional scales, our study explicitly models regional effects of anthropogenic threats and biological traits across the globe. Using phylogenetic comparative methods with a newly-updated supertree of 5020 extant mammals, we investigate the impact of species traits on extinction risk within each WWF ecoregion. Our analyses reveal strong geographical variation in the influence of traits on risk: notably, larger species are at higher risk only in tropical regions. We then relate these patterns to current and recent-historical human impacts across ecoregions using spatial modelling. The body-mass results apparently reflect historical declines of large species outside the tropics due to large-scale land conversion. Narrow-ranged and rare species tend to be at high risk in areas of high current human impacts. The interactions we describe between biological traits and anthropogenic threats increase understanding of the processes determining extinction risk.

Dinosaurs and the Cretaceous Terrestrial Revolution

The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125-80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the group's history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.

A supertree of temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods

As the most diverse group of early tetrapods, temnospondyls provide a unique opportunity to investigate cladogenetic patterns among basal limbed vertebrates. We present five species-level supertrees for temnospondyls, built using a variety of methods. The standard MRP majority rule consensus including minority components shows slightly greater resolution than other supertrees, and its shape matches well several currently accepted hypotheses of higher-level phylogeny for temnospondyls as a whole. Also, its node support is higher than those of other supertrees (except the combined standard plus Purvis MRP supertree). We explore the distribution of significant as well as informative changes (shifts) in branch splitting employing the standard MRP supertree as a reference, and discuss the temporal distribution of changes in time-sliced, pruned trees derived from this supertree. Also, we analyse those shifts that are most relevant to the end-Permian mass extinction. For the Palaeozoic, shifts occur almost invariably along branches that connect major Palaeozoic groups. By contrast, shifts in the Mesozoic occur predominantly within major groups. Numerous shifts bracket narrowly the end-Permian extinction, indicating not only rapid recovery and extensive diversification of temnospondyls over a short time period after the extinction event (possibly less than half a million years), but also the role of intense cladogenesis in the late part of the Permian (although this was counteracted by numerous 'background' extinctions).

The delayed rise of present-day mammals

Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.

Can sexual selection drive female life histories? A comparative study on Galliform birds

Sexual selection has been identified as a major evolutionary force shaping male life history traits but its impact on female life history evolution is less clear. Here we examine the impact of sexual selection on three key female traits (body size, egg size and clutch size) in Galliform birds. Using comparative independent contrast analyses and directional discrete analyses, based on published data and a new genera-level supertree phylogeny of Galliform birds, we investigated how sexual selection [quantified as sexual size dimorphism (SSD) and social mating system (MS)] affects these three important female traits. We found that female body mass was strongly and positively correlated with egg size but not with clutch size, and that clutch size decreased as egg size increased. We established that SSD was related to MS, and then used SSD as a proxy of the strength of sexual selection. We found both a positive relationship between SSD and female body mass and egg size and that increases in female body mass and egg size tend to occur following increases in SSD in this bird order. This pattern of female body mass increases lagging behind changes in SSD, established using our directional discrete analysis, suggests that female body mass increases as a response to increases in the level of sexual selection and not simply through a strong genetic relationship with male body mass. This suggests that sexual selection is linked to changes in female life history traits in Galliformes and we discuss how this link may shape patterns of life history variation among species.

Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets

Nonparamtric bootstrapping methods may be useful for assessing confidence in a supertree inference. We examined the performance of two supertree bootstrapping methods on four published data sets that each include sequence data from more than 100 genes. In "input tree bootstrapping," input gene trees are sampled with replacement and then combined in replicate supertree analyses; in "stratified bootstrapping," trees from each gene's separate (conventional) bootstrap tree set are sampled randomly with replacement and then combined. Generally, support values from both supertree bootstrap methods were similar or slightly lower than corresponding bootstrap values from a total evidence, or supermatrix, analysis. Yet, supertree bootstrap support also exceeded supermatrix bootstrap support for a number of clades. There was little overall difference in support scores between the input tree and stratified bootstrapping methods. Results from supertree bootstrapping methods, when compared to results from corresponding supermatrix bootstrapping, may provide insights into patterns of variation among genes in genome-scale data sets.

Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa

Typically, supertree methods combine a collection of source trees in which just the leaves are labeled by taxa. In such methods the resulting supertree is also leaf labeled. An underlying assumption in these methods is that across all trees in the collection, no two of the taxa are nested; for example, "buttercups" and "plants" are nested taxa. Motivated by Page, the first supertree algorithm for allowing the source trees to collectively have nested taxa is called AncestralBuild. Here, in addition to taxa labeling the leaves, the source trees may have taxa labeling some of their interior nodes. Taxa-labeling interior nodes are at a higher taxonomic level than that of their descendants (for example, genera versus species). Analogous to the supertree method Build for deciding the compatibility of a collection of source trees in which just the leaves are labeled, AncestralBuild is a polynomial-time algorithm for deciding the compatibility of a collection of source trees in which some of the interior nodes are also labeled by taxa. Although a more general method, in this paper we show that the original description of AncestralBuild can be modified so that the running time is as fast as the current fastest running time for Build. Fast computation for deciding compatibility is essential if one is to make use of phylogenetic databases that contain thousands of trees on tens of thousands of taxa. This is particularly so as AncestralBuild is incorporated as a basic tool inside more general supertree methods (that is, methods that always output a tree regardless of the compatibility of the source trees). We apply the method to propose a comprehensive phylogeny of the strepsirrhines, a major group of the primates.

Latent extinction risk and the future battlegrounds of mammal conservation

Global conservation prioritization usually emphasizes areas with highest species richness or where many species are thought to be at imminent risk of extinction. However, these strategies may overlook areas where many species have biological traits that make them particularly sensitive to future human impact but are not yet threatened because such impact is currently low. In this article, we identify such areas for the world's mammals using latent extinction risk, the discrepancy between a species' current extinction risk and that predicted from models on the basis of biological traits. Species with positive latent risk are currently less threatened than their biology would suggest, usually because they inhabit regions or habitats still comparatively unmodified by human activity. Using large new geographic, biological, and phylogenetic databases for nearly 4,000 mammal species, we map the global geographic distribution of latent risk to reveal areas where the mammal fauna is still relatively unthreatened but has high inherent sensitivity to disturbance. These hotspots include large areas such as the Nearctic boreal forests and tundra that are unrepresented in most current prioritization schemes, as well as high-biodiversity areas such as the island arc from Indonesia to the south Pacific. Incorporating latent extinction risk patterns into conservation planning could help guard against future biodiversity loss by anticipating and preventing species declines before they begin.

Molecular and morphological supertree of stony corals (Anthozoa: Scleractinia) using matrix representation parsimony

The supertree algorithm matrix representation with parsimony was used to combine existing hypotheses of coral relationships and provide the most comprehensive species-level estimate of scleractinian phylogeny, comprised of 353 species (27% of extant species), 141 genera (63%) and 23 families (92%) from all seven suborders. The resulting supertree offers a guide for future studies in coral systematics by highlighting regions of concordance and conflict in existing source phylogenies. It should also prove useful in formal comparative studies of character evolution. Phylogenetic effort within Scleractinia has been taxonomically uneven, with a third of studies focussing on the Acroporidae or its most diverse genera. Sampling has also been geographically non-uniform, as tropical, reef-forming taxa have been considered twice as often as non-reef species. The supertree indicated that source trees concur on numerous aspects of coral relationships, such as the division between robust versus complex corals and the distant relationship between families in Archaeocoeniina. The supertree also supported the existence of a large, taxonomically diverse and monophyletic group of corals with many Atlantic representatives having exsert corallites. Another large, unanticipated clade consisted entirely of solitary deep-water species from three families. Important areas of ambiguity include the relationship of Astrocoeniidae to Pocilloporidae and the relative positions of several, mostly deep-water genera of Caryophylliidae. Conservative grafting of species at the base of congeneric groups with uncontroversial monophyletic status resulted in a more comprehensive, though less resolved tree of 1016 taxa.

A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)

Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.

A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants

This paper presents the first complete estimate of the phylogenetic relationships among all 197 species of extant and recently extinct ruminants combining morphological, ethological and molecular information. The composite tree is derived by applying matrix representation using parsimony analysis to 164 previous partial estimates, and is remarkably well resolved, containing 159 nodes (> 80 % of the potential nodes in the completely resolved phylogeny). Bremer decay index has been used to indicate the degree of certainty associated with each clade. The ages of over 80% of the clades in the tree have been estimated from information in the literature. The supertree for Ruminantia illustrates which areas of ruminant phylogeny are still only roughly known because of taxa with controversial relationships (e.g. Odocoileini, Antilopinae) or not studied in great detail (e.g. Muntiacus). It supports the monophyly of the ruminant families and Pecora. According to this analysis Antilocapridae and Giraffidae constitute the superfamily Giraffoidea, which is the sister group of a clade clustering Bovoidea and Cervoidea. The position of several taxa whose systematic positions have remained controversial in the past (Saiga, Pelea, Aepycerus, Pantholops, Ammotragus, Pseudois) is unambiguously established. Nevertheless, the position of Neotragus and Oreotragus within the original radiation of the non-bovine bovids remains unresolved in the present analysis. It also shows that six successive rapid cladogenesis events occurred within the infraorder Pecora during the Oligocene to middle Pliocene, which coincided with periods of global climatic change. Finally, the presented supertree will be a useful framework for comparative and evolutionary biologists interested in studies involving the ruminants.

The evolution of supertrees

Supertrees result from combining many smaller, overlapping phylogenetic trees into a single, more comprehensive tree. As such, supertree construction is probably as old as the field of systematics itself, and remains our only way of visualizing the Tree of Life as a whole. Over the past decade, supertree construction has gained a more formal, objective footing, and has become an area of active theoretical and practical research. Here, I review the history of the supertree approach, focusing mainly on its current implementation. The supertrees of today represent some of the largest, complete phylogenies available for many groups, but are not without their critics. I conclude by arguing that the ever-growing molecular revolution will result in supertree construction taking on a new role and implementation in the future for analyzing large DNA sequence matrices as part of a divide-and-conquer phylogenetic approach.