Cladistic analysis of molecular and morphological data

A new morphological phylogeny of Malacostraca comparing the application of character dependencies and implied weighting

Using a new character matrix composed of revised matrices of previous analyses and new morphological findings, the phylogeny of Malacostraca (Pancrustacea) is analysed anew with 207 characters for 35 terminal taxa across all recognized orders. Particular emphasis was placed on methodological versatility, including different degrees of implied weighting and one of the first applications of methods recently developed in TNT (with the xlinks-command) for considering character dependencies. With >67% of ontological dependencies our character matrix offers a perfect opportunity for putting this new methodology to the test. In particular, we can demonstrate the significant impact of character dependencies and conclusively argue the usefulness of "xlinks" (or the consideration of character dependencies in general). Furthermore, the multimethod framework also enables a comparative evaluation of established and new approaches, and the resulting cladograms thereof. Although our various results leave many questions about the phylogeny of Malacostraca unanswered, clear support is emerging for some monophyla, whereas some surprising findings give reason for methodological reflection. Also, the necessity for an increased attention in terms of taxon sampling and additional character examinations in certain groups becomes obvious. We herein provide (i) an R-function for automatically translating the character dependency syntax proposed by Grams and Richter (Cladistics, 2023, 39, 437) into xlinks-commands for TNT; and (ii) a TNT-script for analysing a character matrix successively under various k-values for implied weighting.

Moving beyond the adaptationist paradigm for human evolution, and why it matters

The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.

Ecological selectivity and the evolution of mammalian substrate preference across the K-Pg boundary

The Cretaceous-Paleogene (K-Pg) mass extinction 66 million years ago was characterized by a worldwide ecological catastrophe and rapid species turnover. Large-scale devastation of forested environments resulting from the Chicxulub asteroid impact likely influenced the evolutionary trajectories of multiple clades in terrestrial environments, and it has been hypothesized to have biased survivorship in favour of nonarboreal lineages across the K-Pg boundary. Here, we evaluate patterns of substrate preferences across the K-Pg boundary among crown group mammals, a group that underwent rapid diversification following the mass extinction. Using Bayesian, likelihood, and parsimony reconstructions, we identify patterns of mammalian ecological selectivity that are broadly similar to those previously hypothesized for birds. Models based on extant taxa indicate predominant K-Pg survivorship among semi- or nonarboreal taxa, followed by numerous independent transitions to arboreality in the early Cenozoic. However, contrary to the predominant signal, some or all members of total-clade Euarchonta (Primates + Dermoptera + Scandentia) appear to have maintained arboreal habits across the K-Pg boundary, suggesting ecological flexibility during an interval of global habitat instability. We further observe a pronounced shift in character state transitions away from plesiomorphic arboreality associated with the K-Pg transition. Our findings are consistent with the hypothesis that predominantly nonarboreal taxa preferentially survived the end-Cretaceous mass extinction, and emphasize the pivotal influence of the K-Pg transition in shaping the early evolutionary trajectories of extant terrestrial vertebrates.

Evolution of protective symbiosis in palaemonid shrimps (Decapoda: Caridea) with emphases on host spectrum and morphological adaptations

Palaemonidae is the most speciose caridean shrimp family, with its huge biodiversity partially generated via symbiosis with various marine invertebrates. Previous studies have provided insights into the evolution of protective symbiosis in this family with evidence for frequent inter-phyla host switches, but the comprehensiveness of evolutionary pathways is hampered by the resolution of the previous phylogenetic trees as well as the taxon coverage. Furthermore, several critical issues related to the evolution of a symbiotic lifestyle, including the change in host spectrum and corresponding morphological adaptations, remain largely unresolved. We therefore performed a much extended phylogenetic comparative study on Palaemonidae, rooted in a comprehensive phylogeny reconstructed by a supermatrix-supertree approach based on a total of three mitochondrial and five nuclear markers. Ancestral state reconstruction of host associations revealed at least three independent evolutions into symbiosis, with potentially a drive to seek protection fuelling incipient symbiosis. Yet, most of the observed symbiotic species diversity was radiated from a single cnidarian associate. The evolution of mandibles and ambulatory dactyli suggests a general lack of correlation with host affiliation (except sponge endosymbionts), implying limited morphological adaptations following host switching, despite being putatively a major adaptive consequence of symbiosis. Our analyses of host spectrum, in terms of basic and taxonomic specificity, revealed no apparent phylogenetic signal but instead resolved a dynamic pattern attributable to frequent host switching. Uncoupling between host spectrum and the degree of morphological specialisation is the norm in palaemonids, suggesting that morphological characters are not fully in tune with host spectrum, in addition to host affiliation. This study demonstrates the complexity in the evolution of symbiosis, pointing to the presence of cryptic adaptations determining host spectrum and governing host switch diversification, and provides a clear direction for the evolutionary study of symbiosis in other marine symbiotic groups involving host switching.

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

Polyphyly of the traditional family Flabellinidae affects a major group of Nudibranchia: aeolidacean taxonomic reassessment with descriptions of several new families, genera, and species (Mollusca, Gastropoda)

The Flabellinidae, a heterogeneous assembly of supposedly plesiomorphic to very derived sea slug groups, have not yet been addressed by integrative studies. Here novel material of rarely seen Arctic taxa as well as North Atlantic, North and South Pacific, and tropical Indo-West Pacific flabellinid species is investigated morpho-anatomically and with multi-locus markers (partial COI, 16S rDNA, 28S rDNA and H3) which were generated and analysed in a comprehensive aeolid taxon sampling. It was found that the current family Flabellinidae is polyphyletic and its phylogeny and taxonomic patterns cannot be understood without considering members from all the Aeolidacean families and, based on a robust phylogenetic hypothesis, morpho-anatomical evolution of aeolids is more complex than suspected in earlier works and requires reclassification of the taxon. Morphological diversity of Flabellinidae is corroborated by molecular divergence rates and supports establishing three new families (Apataidae fam. n., Flabellinopsidae fam. n., Samlidae fam. n.), 16 new genera, 13 new species, and two new subspecies among the former Flabellinidae. Two families, namely Coryphellidae and Paracoryphellidae, are restored and traditional Flabellinidae is considerably restricted. The distinctness of the recently described family Unidentiidae is confirmed by both morphological and molecular data. Several species complexes among all ex-"Flabellinidae" lineages are recognised using both morphological and molecular data. The present study shows that Facelinidae and Aeolidiidae, together with traditional "Tergipedidae", deeply divide traditional "Flabellinidae." Diagnoses for all aeolidacean families are therefore provided and additionally two new non-flabellinid families (Abronicidae fam. n. and Murmaniidae fam. n.) within traditional tergipedids are established to accommodate molecular and morphological disparity. To address relationships and disparity, we propose a new family system for aeolids. Here the aeolidacean species are classified into at least 102 genera and 24 families. Operational rules for integration of morphological and molecular data for taxonomy are suggested.

Solid-phase microextraction-based cuticular hydrocarbon profiling for intraspecific delimitation in Acyrthosiphon pisum

Insect cuticular hydrocarbons (CHCs) play critical roles in reducing water loss and chemical communication. Species-specific CHC profiles have been used increasingly as an excellent character for species classification. However, considerably less is known about their potential for population delimitation within species. The aims of this study were to develop a solid-phase microextraction (SPME)-based CHC collection method and to investigate whether CHC profiles could serve as potential chemotaxonomic tools for intraspecific delimitation in Acyrthosiphon pisum. Optimization of fibers for SPME sampling revealed that 7 μm polydimethylsiloxane (PDMS) demonstrated the most efficient adsorption of CHCs among five different tested fibers. SPME sampling showed good reproducibility with repeated collections of CHCs from a single aphid. Validation of SPME was performed by comparing CHC profiles with those from conventional hexane extractions. The two methods showed no qualitative differences in CHCs, although SPME appeared to extract relatively fewer short-chained CHCs. While CHC profiles of a given population differed among developmental stages, wing dimorphism types, and host plants, wingless adult aphids showed very low variance in relative proportions of individual CHC components. Reproducibility of CHC profiles was explored further to classify wingless adult morphs of A. pisum from five different geographic regions that showed no variation in mitochondrial COI gene sequences. Our results demonstrate that CHC profiles are useful in intraspecific delimitation in the field of insect chemotaxonomy.

At least 23 genera instead of one: the case of Iris L. s.l. (Iridaceae)

BACKGROUND

Iris L. s.l. is one of the most diverse and well-known genera in the Asparagales, with approximately 250-300 circumscribed species and significant economic impact. The taxonomy of the genus has suffered dramatic changes in the last century, particularly in the last decades after the application of molecular techniques. As a result several contrasting systematic arrangements are currently available to taxonomists. Many genera that were split from Iris s.str. in the past, on the basis of morphology (e.g., Hermodactylus, Iridodictyum, Juno, Pardanthopsis, and Xiphion, among others), are now a priori re-included in a very widely circumscribed Iris s.l. (incl. Belamcanda). This resulted in a more heterogeneous genus that is more difficult to define on morphological grounds. Testing congruence between taxonomic treatments and the results of recent molecular studies of Iris has never been performed, mostly due to the lack of proper taxonomic context.

RESULTS

We generated several conventional phylogenies for Iris & outgroups using extensive sampling of taxa (187) and characters (10 plastid loci). We demonstrate that the natural history of Iris, written either as conventional molecular phylogenies or, if viewing in the context of the comparative approach, as a nested most parsimonious hierarchy of patterns, appear to be fully congruent with the narrow taxonomical treatment of the genus, restricted to the rhizomatous "bearded" taxa. The resulting topologies place Belamcanda, Pardanthopsis, and Gattenhofia as sisters to Iris s.str. and genus Siphonostylis as sister to Iris s.l.

CONCLUSION

The present study clearly justifies the splitting of Iris s.l. into at least 23 genera, 18 of which have already been accepted in the past by numerous authorities. These genera are characterized by unique combinations of partly overlapping morphological characters and biogeography. Moreover, nearly the same entities, which we here recognize at a generic rank, were for centuries frequently referred to by horticulturists as "working-name" groups.

Phylogenetic supertrees: Assembling the trees of life

Systematists and comparative biologists commonly want to make statements about relationships among taxa that have never been collectively included in any single phylogenetic analysis. Construction of phylogenetic 'supertrees' provides one solution. Supertrees are estimates of phylogeny assembled from sets of smaller estimates (source trees) sharing some but not necessarily all their taxa in common. If certain conditions are met, supertrees can retain all or most of the information from the source trees and also make novel statements about relationships of taxa that do not co-occur on any one source tree. Supertrees have commonly been constructed using subjective and informal approaches, but several explicit approaches have recently been proposed.

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.

Comparative analysis of chromosome counts infers three paleopolyploidies in the mollusca

The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

BACKGROUND

The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them.

RESULTS

Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches.

CONCLUSIONS

Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

Phylogenomic dating--a method of constraining the age of microbial taxa that lack a conventional fossil record

A phylogenomic dating approach was used to identify potential age constraints for multiple archaeal groups, many of which have no fossil, isotopic, or biomarker record. First, well-resolved phylogenetic trees were inferred with the use of multiple gene sequences obtained from whole genome sequences. Next, the ability to use oxygen as a terminal electron acceptor was coded into characters, and ancestral state reconstruction was used to identify clades with taxa that metabolize oxygen and likely had an aerobic ancestor. Next, the habitat of the ancestor was inferred. If the local presence of Cyanobacteria could be excluded from the putative ancestral habitat, then these clades would have originated after the rise in atmospheric oxygen 2.32 Ga. With this method, an upper age of 2.32 Ga (an "oxygen age constraint") is proposed for four major archaeal clades: the Sulfolobales, Thermoplasmatales, Thermoproteus neutrophilus/Pyrobaculum spp., and the Thermoproteales. It was also shown that the halophilic archaea likely had an aerobic common ancestor, yet the possibility of local oxygen oases before oxygenation of the atmosphere could not be formally rejected. Thus, an oxygen age constraint was not assessed for this group. This work suggests that many archaeal groups are not as ancient as many in the research community have previously assumed, and it provides a new method for establishing upper age constraints for major microbial groups that lack a conventional fossil record.

Phylogenomic dating--the relative antiquity of archaeal metabolic and physiological traits

Ancestral trait reconstruction was used to identify the relative ancestry of metabolic and physiological traits in the archaeal domain of life. First, well-resolved phylogenetic trees were inferred with multiple gene sequences obtained from whole genome sequences. Next, metabolic and physiological traits were coded into characters, and ancestral state reconstruction was used to identify ancient and derived traits. Traits inferred to be ancient included sulfur reduction, methanogenesis, and hydrogen oxidation. By using the articulation of the "oxygen age constraint," several other traits were inferred to have arisen at or after 2.32 Ga: aerobic respiration, nitrate reduction, sulfate reduction, thiosulfate reduction, sulfur oxidation, and sulfide oxidation. Complex organic metabolism appeared to be nearly as ancient as autotrophy. Hyperthermophily was ancestral, while hyperacidophily and extreme halophily likely arose after 2.32 Ga. The ancestral euryarchaeote was inferred to have been a hyperthermophilic marine methanogen that lived in a deep-sea hydrothermal vent. In contrast, the ancestral crenarchaeote was most likely a hyperthermophilic sulfur reducer that lived in a slightly acidic terrestrial environment, perhaps a fumarole. Cross-colonization of these habitats may not have occurred until after 2.32 Ga, which suggests that both archaeal lineages exhibited niche specialization on early Earth for a protracted period of time.

Phylogeny of marattioid ferns (Marattiaceae): inferring a root in the absence of a closely related outgroup

Closely related outgroups are optimal for rooting phylogenetic trees; however, such ideal outgroups are not always available. A phylogeny of the marattioid ferns (Marattiaceae), an ancient lineage with no close relatives, was reconstructed using nucleotide sequences of multiple chloroplast regions (rps4 + rps4-trnS spacer, trnS-trnG spacer + trnG intron, rbcL, atpB), from 88 collections, selected to cover the broadest possible range of morphologies and geographic distributions within the extant taxa. Because marattioid ferns are phylogenetically isolated from other lineages, and internal branches are relatively short, rooting was problematic. Root placement was strongly affected by long-branch attraction under maximum parsimony and by model choice under maximum likelihood. A multifaceted approach to rooting was employed to isolate the sources of bias and produce a consensus root position. In a statistical comparison of all possible root positions with three different outgroups, most root positions were not significantly less optimal than the maximum likelihood root position, including the consensus root position. This phylogeny has several important taxonomic implications for marattioid ferns: Marattia in the broad sense is paraphyletic; the Hawaiian endemic Marattia douglasii is most closely related to tropical American taxa; and Angiopteris is monophyletic only if Archangiopteris and Macroglossum are included.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes

A comprehensive phylogeny of papilionoid legumes was inferred from sequences of 2228 taxa in GenBank release 147. A semiautomated analysis pipeline was constructed to download, parse, assemble, align, combine, and build trees from a pool of 11,881 sequences. Initial steps included all-against-all BLAST similarity searches coupled with assembly, using a novel strategy for building length-homogeneous primary sequence clusters. This was followed by a combination of global and local alignment protocols to build larger secondary clusters of locally aligned sequences, thus taking into account the dramatic differences in length of the heterogeneous coding and noncoding sequence data present in GenBank. Next, clusters were checked for the presence of duplicate genes and other potentially misleading sequences and examined for combinability with other clusters on the basis of taxon overlap. Finally, two supermatrices were constructed: a "sparse" matrix based on the primary clusters alone (1794 taxa x 53,977 characters), and a somewhat more "dense" matrix based on the secondary clusters (2228 taxa x 33,168 characters). Both matrices were very sparse, with 95% of their cells containing gaps or question marks. These were subjected to extensive heuristic parsimony analyses using deterministic and stochastic heuristics, including bootstrap analyses. A "reduced consensus" bootstrap analysis was also performed to detect cryptic signal in a subtree of the data set corresponding to a "backbone" phylogeny proposed in previous studies. Overall, the dense supermatrix appeared to provide much more satisfying results, indicated by better resolution of the bootstrap tree, excellent agreement with the backbone papilionoid tree in the reduced bootstrap consensus analysis, few problematic large polytomies in the strict consensus, and less fragmentation of conventionally recognized genera. Nevertheless, at lower taxonomic levels several problems were identified and diagnosed. A large number of methodological issues in supermatrix construction at this scale are discussed, including detection of annotation errors in GenBank sequences; the shortage of effective algorithms and software for local multiple sequence alignment; the difficulty of overcoming effects of fragmentation of data into nearly disjoint blocks in sparse supermatrices; and the lack of informative tools to assess confidence limits in very large trees.

Evolution of carnivory in Lentibulariaceae and the Lamiales

As a basis for analysing the evolution of the carnivorous syndrome in Lentibulariaceae (Lamiales), phylogenetic reconstructions were conducted based on coding and non-coding chloroplast DNA (matK gene and flanking trnK intron sequences, totalling about 2.4 kb). A dense taxon sampling including all other major lineages of Lamiales was needed since the closest relatives of Lentibulariaceae and the position of "proto-carnivores" were unknown. Tree inference using maximum parsimony, maximum likelihood, and Bayesian approaches resulted in fully congruent topologies within Lentibulariaceae, whereas relationships among the different lineages of Lamiales were only congruent between likelihood and Bayesian optimizations. Lentibulariaceae and their three genera (Pinguicula, Genlisea, and Utricularia) are monophyletic, with Pinguicula being sister to a Genlisea-Utricularia clade. Likelihood and Bayesian trees converge on Bignoniaceae as sister to Lentibulariaceae, albeit lacking good support. The "proto-carnivores" (Byblidaceae, Martyniaceae) are found in different positions among other Lamiales but not as sister to the carnivorous Lentibulariaceae, which is also supported by Khishino-Hasegawa tests. This implies that carnivory and its preliminary stages ("proto-carnivores") independently evolved more than once among Lamiales. Ancestral states of structural characters connected to the carnivorous syndrome are reconstructed using the molecular tree, and a hypothesis on the evolutionary pathway of the carnivorous syndrome in Lentibulariaceae is presented. Extreme DNA mutational rates found in Utricularia and Genlisea are shown to correspond to their unusual nutritional specialization, thereby hinting at a marked degree of carnivory in these two genera.

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.

Integrating the genotype and phenotype in hominid paleontology

Competing interpretations of human origins and evolution have recently proliferated despite the accelerated pace of fossil discovery. These controversies parallel those involving other vertebrate families and result from the difficulty of studying evolution among closely related species. Recent advances in developmental and quantitative genetics show that some conventions routinely used by hominid and other mammalian paleontologists are unwarranted. These same advances provide ways to integrate knowledge of the genotype into the study of the phenotype. The result is an approach that promises to yield a fuller understanding of evolution below the family level.

Fossil sister group of craniates: predicted and found

This study investigates whether the recently described Cambrian fossil Haikouella (and the very similar Yunnanozoon) throws light on the longstanding problem of the origin of craniates. In the first rigorous cladistic analysis of the relations of this animal, we took 40 anatomical characters from Haikouella and other taxa (hemichordates, tunicates, cephalochordates, conodont craniates and other craniates, plus protostomes as the outgroup) and subjected these characters to parsimony analysis. The characters included several previously unrecognized traits of Haikouella, such as upper lips resembling those of larval lampreys, the thick nature of the branchial bars, a mandibular branchial artery but no mandibular branchial bar, muscle fibers defining the myomeres, a dark fibrous sheath that defines the notochord, conclusive evidence for paired eyes, and a large hindbrain and diencephalon in the same positions as in the craniate brain. The cladistic analysis produced this tree: (protostomes, hemichordates (tunicates, (cephalochordates, (Haikouella, (conodonts + other craniates))))), with the "Haikouella + craniate" clade supported by bootstrap values that ranged from 81-96%, depending on how the analysis was structured. Thus, Haikouella is concluded to be the sister group of the craniates. Alternate hypotheses that unite Haikouella with hemichordates or cephalochordates, or consider it a basal deuterostome, received little or no support. Although it is the sister group of craniates, Haikouella is skull-less and lacks an ear, but it does have neural-crest derivatives in its branchial bars. Its craniate characters occur mostly in the head and pharynx; its widely spaced, robust branchial bars indicate it ventilated with branchiomeric muscles, not cilia. Despite its craniate mode of ventilation, Haikouella was not a predator but a suspension feeder, as shown by its cephalochordate-like endostyle, and tentacles forming a screen across the mouth. Haikouella was compared to pre-craniates predicted by recent models of craniate evolution and was found to fit these predictions closely. Specifically, it fits Northcutt and Gans' prediction that the change from ciliary to muscular ventilation preceded the change from suspension feeding to predatory feeding; it fits Butler's claim that vision was the first craniate sense to start elaborating; it is consistent with the ideas of Donoghue and others about the ancestor of conodont craniates; and, most strikingly, it resembles Mallatt's prediction of the external appearance of the ancestral craniate head. By contrast, Haikouella does not fit the widespread belief that ancestral craniates resembled hagfishes, because it has no special hagfish characters. Overall, Haikouella agrees so closely with recent predictions about pre-craniates that we conclude that the difficult problem of craniate origins is nearly solved.

Cuticular hydrocarbons suggest three lineages in Reticulitermes (Isoptera: Rhinotermitidae) from North America

Cuticular hydrocarbon mixtures can be used to discriminate insect taxa. They have utility for determining phylogenetic relationships where they are independent characters with discrete states and represent a hierarchical distribution of shared, derived characters. We report inferred degrees of relatedness among the chemical phenotypes of Reticulitermes from PAUP (phylogenetic analysis using parsimony) analyses of cuticular hydrocarbon characters. One hundred and forty-one Reticulitermes colonies collected from California, Georgia, New Mexico, Arizona and Nevada were used. Initial maximum parsimony analyses sorted the 141 colonies into 26 chemical phenotypes. Subsequent analyses, using the ancestral species Coptotermes formosanus and Heterotermes sp. as outgroups, sorted Reticulitermes taxa into three major lineages, each characterized by a different set of dominant methyl-branched or unsaturated hydrocarbon components. Reticulitermes in lineage I have cuticular hydrocarbon mixtures with a preponderance of internally branched monomethylalkanes and 11,15-dimethylalkanes. Those in lineage II are defined by a preponderance of 5-methylalkanes and 5,17-dimethylalkanes. Taxa in lineage III are characterized by the predominance of olefins and a relative paucity of n-alkanes and methyl-branched alkanes. Bootstrap analyses and decay indices provided statistical support and robustness for these chemical-based relationships.

Evaluation of fluorescence-based amplified fragment length polymorphism analysis for molecular typing in hospital epidemiology: comparison with pulsed-field gel electrophoresis for typing strains of vancomycin-resistant Enterococcus faecium

Fluorescence-based amplified fragment length polymorphism (fbAFLP) is a novel assay based on the fluorescent analysis of an amplified subset of restriction fragments. The fbAFLP assay involves the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The ligation of adapters with primer-specific sites coupled with primers containing selective nucleotides allowed the full potential of PCR to be realized while maintaining the advantages of restriction endonuclease analysis. Fluorescence-based fragment analysis with polyacrylamide gel electrophoresis provides the accurate band sizing required for homology assessment. The large number of phylogenetically informative characters obtained by fbAFLP is well suited for cluster analysis and database development. The method demonstrated excellent reproducibility and ease of performance and interpretation. We typed 30 epidemiologically well-characterized isolates of vancomycin-resistant enterococci from an outbreak in a university hospital by fbAFLP. Clustering of fbAFLP data matched epidemiological, microbiological, and pulsed-field gel electrophoresis data. This study demonstrates the unprecedented utility of fbAFLP for epidemiological investigation. Future developments in standardization and automation will set fbAFLP as the "gold standard" for molecular typing in epidemiology.

Recent progress in reconstructing angiosperm phylogeny

In the past year, the study of angiosperm phylogeny has moved from tentative inferences based on relatively small data matrices into an era of sophisticated, multigene analyses and significantly greater confidence. Recent studies provide both strong statistical support and mutual corroboration for crucial aspects of angiosperm phylogeny. These include identifying the earliest extant lineages of angiosperms, confirming Amborella as the sister of all other angiosperms, confirming some previously proposed lineages and redefining other groups consistent with their phylogeny. This phylogenetic framework enables the exploration of both genotypic and phenotypic diversification among angiosperms.

Factors influencing phylogenetic inference: a case study using the mammalian carnivores

Phylogenetic reconstruction has undergone numerous developments in tree selection criteria (e.g., phenetics, cladistics, maximum-likelihood), available data sources (morphology versus molecules, and subsets of the latter), and practical limits on study size. Together with study age, I examined the effects of these variables on inferences of phylogeny for the mammalian order Carnivora. The raw data comprised 274 source trees spread among 13 carnivore taxa (generally families), which I divided into categories for each variable and combined using the supertree technique matrix representation with parsimony analysis. Incongruence between the resultant tree topologies or the underlying data was assessed using four comparison measures, each with slightly different properties: the triplet measures "do not conflict" and "explicitly agree," the partition metric, and the incongruence length difference metric. Except for a few cases reflecting historical problem areas in carnivore systematics, no significant differences in incongruence levels were found among the different categories within each variable, between the variables themselves, or between the taxa. Thus, most estimates of carnivore phylogeny cannot be distinguished from one another (and may even point toward the same solution) regardless of the methodology or data source employed. This conclusion held regardless of the comparison measure used.

Structure of the large subunit rDNA from a diatom, and comparison between small and large subunit ribosomal RNA for studying stramenopile evolution

The aim of this study was to compare the usefulness of complete small and large subunit rRNA, and a combination of both molecules, for reconstructing stramenopile evolution. To this end, phylogenies from species of which both sequences are known were constructed with the neighbor-joining, maximum parsimony, and maximum likelihood methods. Also the use of structural features of the rRNAs was evaluated. The large subunit rRNA from the diatom Skeletonema pseudocostatum was sequenced in order to have a more complete taxon sampling, and a group I intron was identified. Our results indicated that heterokont algae are monophyletic, with diatoms diverging first. However, as the analysis was restricted to a particular data set containing merely six taxa, the outcome has limited value for elucidating stramenopile relationships. On the other hand, this approach permits comparison of the performance of both rRNA molecules without interference from other factors, such as a different species selection for each molecule. For the taxa used, the large subunit rRNA clearly contained more phylogenetic information than the small subunit rRNA. Although this result can definitely not be generalized and depends on the phylogeny to be studied, in some cases determining complete large subunit rRNA sequences certainly seems worthwhile.

Nuclear ribosomal DNA evidence for a western North American origin of Hawaiian and South American species of Sanicula (Apiaceae)

Results from phylogenetic analysis of nuclear rDNA internal transcribed spacer (ITS) sequences from a worldwide sample of Sanicula indicate that Hawaiian sanicles (Sanicula sect. Sandwicenses) constitute a monophyletic group that descended from a western North American ancestor in Sanicula sect. Sanicoria, a paraphyletic assemblage of mostly Californian species. A monophyletic group comprising representatives of all 15 species of S. sect. Sanicoria and the three sampled species of S. sect. Sandwicenses was resolved in all maximally parsimonious trees, rooted with sequences from species of Astrantia and Eryngium. All sequences sampled from eastern North American, European, and Asian species of Sanicula fell outside the ITS clade comprising S. sect. Sanicoria and S. sect. Sandwicenses. A lineage comprising the Hawaiian taxa and three species endemic to coastal or near-coastal habitats in western North America (Sanicula arctopoides, Sanicula arguta, and Sanicula laciniata) is diagnosed by nucleotide substitutions and a 24-bp deletion in ITS2. The hooked fruits in Sanicula lead us to conclude that the ancestor of Hawaiian sanicles arrived from North America by external bird dispersal; similar transport has been hypothesized for the North American tarweed ancestor of the Hawaiian silversword alliance (Asteraceae). Two additional long-distance dispersal events involving members of S. sect. Sanicoria can be concluded from the ITS phylogeny: dispersal of Sanicula crassicaulis and Sanicula graveolens from western North America to southern South America.

The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types

The 18S rRNA gene (Rns) phylogeny of Acanthamoeba is being investigated as a basis for improvements in the nomenclature and taxonomy of the genus. We previously analyzed Rns sequences from 18 isolates from morphological groups 2 and 3 and found that they fell into four distinct evolutionary lineages we called sequence types T1-T4. Here, we analyzed sequences from 53 isolates representing 16 species and including 35 new strains. Eight additional lineages (sequence types T5-T12) were identified. Four of the 12 sequence types included strains from more than one nominal species. Thus, sequence types could be equated with species in some cases or with complexes of closely related species in others. The largest complex, sequence type T4, which contained six closely related nominal species, included 24 of 25 keratitis isolates. Rns sequence variation was insufficient for full phylogenetic resolution of branching orders within this complex, but the mixing of species observed at terminal nodes confirmed that traditional classification of isolates has been inconsistent. One solution to this problem would be to equate sequence types and single species. Alternatively, additional molecular information will be required to reliably differentiate species within the complexes. Three sequence types of morphological group 1 species represented the earliest divergence in the history of the genus and, based on their genetic distinctiveness, are candidates for reclassification as one or more novel genera.

Consistency, characters, and the likelihood of correct phylogenetic inference

Computer simulations of character-state evolution in 8, 16, 32, and 64 ingroup taxa with a known set of relationships demonstrate that the maximum probability of correct phylogenetic inference increases with the number of variable (or informative) characters and their consistency index and decreases with the number of taxa, when the consistency index has been standardized to eliminate its dependence on the number of taxa. Equations for the probability of correct phylogenetic inference and for the standardized consistency indices (including or excluding autapomorphies) are derived. Given that actual studies based on DNA restriction sites and sequences generate more characters with a higher level of consistency than comparable studies based on morphology, calculations suggest that such molecular studies may often provide a more precise guide to phylogenetic relationships.