Archaeobatrachian paraphyly and pangaean diversification of crown-group frogs

Current models for the early diversification of living frogs inferred from morphological, ontogenetic, or DNA sequence data invoke very different scenarios of character evolution and biogeography. To explore central controversies on the phylogeny of Anura, we analyzed nearly 4000 base pairs of mitochondrial and nuclear DNA for the major frog lineages. Likelihood-based analyses of this data set are congruent with morphological evidence in supporting a paraphyletic arrangement of archaeobatrachian frogs, with an (Ascaphus + Leiopelma) clade as the sister-group of all other living anurans. The stability of this outcome is reinforced by screening for phylogenetic bias resulting from site-specific rate variation, homoplasy, or the obligatory use of distantly related outgroups. Twenty-one alternative branching and rooting hypotheses were evaluated using a nonparametric multicomparison test and parametric bootstrapping. Relaxed molecular clock estimates situate the emergence of crown-group anurans in the Triassic, approximately 55 million years prior to their first appearance in the fossil record. The existence of at least four extant frog lineages on the supercontinent Pangaea before its breakup gains support from the estimation that three early splits between Laurasia- and Gondwana-associated families coincide with the initial rifting of these landmasses. This observation outlines the potential significance of this breakup event in the formation of separate Mesozoic faunal assemblages in both hemispheres.     

Reconstructing the evolution of umbonal sculptures in the Unionida

‘Umbonal sculptures’ of freshwater mussels (Unionida), which ornament the early ontogenetic shell, have long been used for species identification. Specificity of these sculptures to higher taxonomic levels and their value for phylogenetic reconstruction are still under considerable scientific debate. In particular, the distribution of beak sculpture morphotypes across the unionoid phylogeny and, consequently, evolution of this character remain poorly understood. Based on an examination of 187 taxa, covering five of the six extant unionoid families, this study presents a new model of character evolution of umbonal sculptures in the order. Ten morphotypes were recognized and conceptualized into the cladistic characters sculpture presence and category. Optimization of sculpture presence on two recent hypotheses of palaeoheterodont phylogenetic relationships using the program Mesquite indicates a sculptured common ancestor of the extant Unionida, with multiple losses of the umbonal ornament occurring subsequently within the clade. Reconstruction of changes in sculpture category is ambiguous and demonstrates the need for further research into the evolutionary relationships of freshwater mussels in general and of their early ontogenetic sculptures in particular. Ambiguity is reduced in analyses applying a model with unequal costs of transformation between character states, which was derived from observations on intermediate forms and polymorphisms. These analyses suggest ‘V‐shaped’ or ‘nodulous’ sculpture as the plesiomorphic sculptural category for Unionida. The relatively low levels of homoplasy inferred for V‐shaped, pseudo‐radial and double‐looped sculptures suggest that these types may comprise useful guides to relationships within Unionida. The high degree of homoplasy of W‐shaped, pseudo‐concentric, wrinkled and single‐looped sculptures, on the other hand, renders these sculpture types less fit for such purposes.     

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.     

Complicated evolution of the caprellid (Crustacea: Malacostraca: Peracarida: Amphipoda) body plan,reacquisition or multiple losses of the thoracic limbs and pleons

The Caprellidea (Crustacea) have undergone an interesting morphological evolution from their ancestral gammarid-like form. Although most caprellid families have markedly reduced third and fourth pereopods (the walking thoracic limbs) and pleons (the posterior body parts), one family, Caprogammaridae, has developed pleon with swimming appendages (pleopods), whereas another family, Phtisicidae, possesses well-developed functional third and fourth pereopods. The unique character status of these families implies that there has been reacquisition or multiple losses of both pereopods and the pleon within the Caprellidea lineages. Although the Caprellidea are fascinating animals for the study of morphological evolution, the phylogenetic relationships among the Caprellidea are poorly understood. One obstacle to studying the evolution of the Caprellidea is the difficulty of collecting samples of caprogammarid species. In this study, we obtained live samples of a Caprogammaridae species and confirmed that its pleon and pleopods could perform similar locomotive functions and swimming movements as observed in gammarids. From the phylogenetic analyses on 18S ribosomal RNA gene sequences, we identified three distinct clades of Caprellidea. The ancestral state reconstruction based on the obtained phylogeny suggested that once lost, the third and fourth pereopods were regained in the Phtisicidae, while the pleon was regained in the Caprogammaridae, while we could not exclude the possibility of independent losses. In either case, the caprellid lineage underwent a quite complicated morphological evolution, and possibly the Caprellidea may be an exception to Dollo’s law.     

Phylogeny of Ensifera (Hexapoda: Orthoptera) using three ribosomal loci, with implications for the evolution of acoustic communication

Representatives of the Orthopteran suborder Ensifera (crickets, katydids, and related insects) are well known for acoustic signals produced in the contexts of courtship and mate recognition. We present a phylogenetic estimate of Ensifera for a sample of 51 taxonomically diverse exemplars, using sequences from 18S, 28S, and 16S rRNA. The results support a monophyletic Ensifera, monophyly of most ensiferan families, and the superfamily Gryllacridoidea which would include Stenopelmatidae, Anostostomatidae, Gryllacrididae, and Lezina. Schizodactylidae was recovered as the sister lineage to Grylloidea, and both Rhaphidophoridae and Tettigoniidae were found to be more closely related to Grylloidea than has been suggested by prior studies. The ambidextrously stridulating haglid Cyphoderris was found to be basal (or sister) to a clade that contains both Grylloidea and Tettigoniidae. Tree comparison tests with the concatenated molecular data found our phylogeny to be significantly better at explaining our data than three recent phylogenetic hypotheses based on morphological characters. A high degree of conflict exists between the molecular and morphological data, possibly indicating that much homoplasy is present in Ensifera, particularly in acoustic structures. In contrast to prior evolutionary hypotheses based on most parsimonious ancestral state reconstructions, we propose that tegminal stridulation and tibial tympana are ancestral to Ensifera and were lost multiple times, especially within the Gryllidae.     

Acanthocephalan phylogeny and the evolution of parasitism

The study of parasite evolution relies on the identification of free-living sister taxa of parasitic lineages. Most lineages of parasitic helminths are characterized by an amazing diversity of species that complicates the resolution of phylogenetic relationships. Acanthocephalans offer a potential model system to test various long-standing hypotheses and generalizations regarding the evolution of parasitism in metazoans. The entirely parasitic Acanthocephala have a diversity of species that is manageable with regards to constructing global phylogenetic hypotheses, exhibit variation in hosts and habitats, and are hypothesized to have close phylogenetic affinities to the predominately free-living Rotifera. In this paper, I review and test previous hypotheses of acanthocephalan phylogenetic relationships with analyses of the available 18S rRNA sequence database. Maximum-parsimony and maximum-likelihood inferred trees differ significantly with regard to relationships among acanthocephalans and rotifers. Maximum-parsimony analysis results in a paraphyletic Rotifera, placing a long-branched bdelloid rotifer as the sister taxon of Acanthocephala. Maximum-likelihood analysis results in a monophyletic Rotifera. The difference between the two optimality criteria is attributed to long-branch attraction. The two analyses are congruent in terms of relationships within Acanthocephala. The three sampled classes are monophyletic, and the Archiacanthocephala is the sister taxon of a Palaeacanthocephala + Eoacanthocephala clade. The phylogenetic hypothesis is used to assess the evolution of host and habitat preferences. Acanthocephalan lineages have exhibited multiple radiations into terrestrial habitats and bird and mammal definitive hosts from ancestral aquatic habitats and fish definitive hosts, while exhibiting phylogenetic conservatism in the type of arthropod intermediate host utilized.     

On the incidence of intron loss and gain in paralogous gene families

Understanding gene duplication and gene structure evolution are fundamental goals of molecular evolutionary biology. A previous study by Babenko et al. (2004. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res. 32:3724-3733) employed Dollo parsimony to infer spliceosomal intron losses and gains in paralogous gene families and concluded that there was a general excess of gains over losses. This result contrasts with patterns in orthologous genes, in which most lineages show an excess of intron losses over gains, suggesting the possibility of fundamentally different modes of intron evolution between orthologous and paralogous genes. We further studied the data and found a low level of intron position conservation with outgroups, and this led to problems with using Dollo parsimony to analyze the data. Statistical reanalysis of the data suggests, instead, that intron losses have outnumbered intron gains in paralogous gene families.     

300 million years of diversification: elucidating the patterns of orthopteran evolution based on comprehensive taxon and gene sampling

Orthoptera is the most diverse order among the polyneopteran groups and includes familiar insects, such as grasshoppers, crickets, katydids, and their kin. Due to a long history of conflicting classification schemes based on different interpretations of morphological characters, the phylogenetic relationships within Orthoptera are poorly understood and its higher classification has remained unstable. In this study, we establish a robust phylogeny of Orthoptera including 36 of 40 families representing all 15 currently recognized superfamilies and based on complete mitochondrial genomes and four nuclear loci, in order to test previous phylogenetic hypotheses and to provide a framework for a natural classification and a reference for studying the pattern of divergence and diversification. We find strong support for monophyletic suborders (Ensifera and Caelifera) as well as major superfamilies. Our results corroborate most of the higher‐level relationships previously proposed for Caelifera, but suggest some novel relationships for Ensifera. Using fossil calibrations, we provide divergence time estimates for major orthopteran lineages and show that the current diversity has been shaped by dynamic shifts of diversification rates at different geological times across different lineages. We also show that mitochondrial tRNA gene orders have been relatively stable throughout the evolutionary history of Orthoptera, but a major tRNA gene rearrangement occurred in the common ancestor of Tetrigoidea and Acridomorpha, thereby representing a robust molecular synapomorphy, which has persisted for 250 Myr.     

Keeping it simple: flowering plants tend to retain, and revert to, simple leaves

? A wide range of factors (developmental, physiological, ecological) with unpredictable interactions control variation in leaf form. Here, we examined the distribution of leaf morphologies (simple and complex forms) across angiosperms in a phylogenetic context to detect patterns in the directions of changes in leaf shape. ? Seven datasets (diverse angiosperms and six nested clades, Sapindales, Apiales, Papaveraceae, Fabaceae, Lepidium, Solanum) were analysed using maximum likelihood and parsimony methods to estimate asymmetries in rates of change among character states. ? Simple leaves are most frequent among angiosperm lineages today, were inferred to be ancestral in angiosperms and tended to be retained in evolution (stasis). Complex leaves slowly originated ('gains') and quickly reverted to simple leaves ('losses') multiple times, with a significantly greater rate of losses than gains. Lobed leaves may be a labile intermediate step between different forms. The nested clades showed mixed trends; Solanum, like the angiosperms in general, had higher rates of losses than gains, but the other clades had higher rates of gains than losses. ? The angiosperm-wide pattern could be taken as a null model to test leaf evolution patterns in particular clades, in which patterns of variation suggest clade-specific processes that have yet to be investigated fully.     

Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda,Insecta) and implications for their higher systematics

A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets, and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single, fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree that lacked several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets, which identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis: comparative analysis of trees recovered from resampled data sets, and the application of a randomization test. Because the results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups, using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the maximum likelihood criteria is the most discriminating approach for the combined sequences. The results indicate, moreover, that the caeliferan Pneumoroidea and Pamphagoidea, as previously suggested, are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.     

Sequences of 72 plastid genes support the early divergence of Cornales in the asterids

Recent phylogenetic analyses of molecular data have supported different hypotheses of relationships among Cornales,Ericales,and core asterids.Such hypotheses have implications for the evolution of important morphological and embryological features of asterids.In this study we generated plastid genome-scale data of Davidia (Cornales) and Franklinia (Ericales) and combined them with published sequence data of eudicots.Our maximum parsimony,maximum likelihood,and Bayesian analyses generated strongly supported and congruent phylogenetic relationships among the three major lineages of the asterids.Cornales diverges first in asterids; Ericales is sister to the core asterids.Adding two more taxa helps mitigate long branch attraction in parsimony analyses.Sampling 26-28 plastid protein-coding genes may provide satisfactory resolution and support for relationships of eudicots including basal lineages of asterids.     

A bi-organellar phylogenomic study of Pandanales: inference of higher-order relationships and unusual rate-variation patterns

We used a bi-organellar phylogenomic approach to address higher-order relationships in Pandanales, including the first molecular phylogenetic study of the panama-hat family, Cyclanthaceae. Our genus-level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellar genomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid-based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well-supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non-photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.     

Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes

The evolution of two mitochondrial genes, cytochrome b and cytochrome c oxidase subunit II, was examined in several eutherian mammal orders, with special emphasis on the orders Artiodactyla and Rodentia. When analyzed using both maximum parsimony, with either equal or unequal character weighting, and neighbor joining, neither gene performed with a high degree of consistency in terms of the phylogenetic hypotheses supported. The phylogenetic inconsistencies observed for both these genes may be the result of several factors including differences in the rate of nucleotide substitution among particular lineages (especially between orders), base composition bias, transition/transversion bias, differences in codon usage, and different constraints and levels of homoplasy associated with first, second, and third codon positions. We discuss the implications of these findings for the molecular systematics of mammals, especially as they relate to recent hypotheses concerning the polyphyly of the order Rodentia, relationships among the Artiodactyla, and various interordinal relationships.Correspondence to: R.L. Honeycutt     

Choosing among alternative trees of multigene families

Estimation of gene trees is the first step in testing alternative hypotheses about the evolution of multigene families. The standard practice for inferring gene family history is to construct trees that meet some objective criteria based on the fit of the character state changes (nucleotide or amino acid changes) to the gene tree. Unfortunately, analysis of character state data can be misleading. In addition, this approach ignores information about the relationships of the species from which the genes have been sampled. In this paper I explore using statistics of fit between the character data and gene trees and the reconciliation of the gene and species trees for choosing among alternative evolutionary hypotheses of gene families. In particular, I advocate a two-pronged strategy for choosing among alternative gene trees. First, the character data are used to define a set of acceptable gene trees (i.e., trees that are not significantly different from the minimum length tree). Next, the set of acceptable gene trees is reconciled with a known species tree, and the gene tree requiring the fewest number of gene duplications and losses is adopted as the best estimate of evolutionary history. The approach is illustrated using three gene families: BMP, EGR, and LDH.     

Are mimics monophyletic? The necessity of phylogenetic hypothesis tests in character evolution

Background  

The processes governing the origin and maintenance of mimetic phenotypes can only be understood in a phylogenetic framework. Phylogenetic estimates of evolutionary relationships can provide a context for analyses of character evolution; however, when phylogenetic estimates conflict, rigorous analyses of alternative evolutionary histories are necessary to determine the likelihood of a specific history giving rise to the observed pattern of diversity. The polyphenic butterfly Limenitis arthemis provides a case in point. This species is comprised of three lineages, two of which are mimetic and one of which is non-mimetic. Conflicting estimates of the relationships among these three lineages requires direct evaluation of the alternative hypotheses of mimicry evolution.     

Strengths and limitations of molecular sequence comparisons for inferring the phylogeny of the major groups of fishes

Although the phylogenetic relationships of the major groups of fishes have been extensively studied with morphological characters, not all have been convincingly resolved. Analyses of molecular sequences from these groups may provide additional insights into problematical relationships, but are only just beginning to appear. We compare our own results from analyses of 18s ribosomal RNA sequences with those of other studies using globins, parvalbumins, insulin, 28s ribosomal RNA, and portions of two mitochondria1 genes (12S ribosomal RNA and cytochrome b ). Our evaluation of these studies reveals some of the difficulties encountered in reconstructing ancient divergences within the fishes, including unequal rates of evolution (among regions of a molecule as well as among lineages), gene duplication, extinction of lineages, and a possible rapid radiation of gnathostome higher taxa. The importance of evaluating the robustness of particular phylogenetic hypotheses is stressed. Some molecules appear to be inappropriate for investigating higher level divergences within the fishes; others are more promising, but must be examined in more taxa to allow an adequate evaluation of their utility. Convincing support for particular hypotheses of relationship will ultimately require congruence of trees generated from independent molecular data sets.     

Prevalence of intron gain over intron loss in the evolution of paralogous gene families

The mechanisms and evolutionary dynamics of intron insertion and loss in eukaryotic genes remain poorly understood. Reconstruction of parsimonious scenarios of gene structure evolution in paralogous gene families in animals and plants revealed numerous gains and losses of introns. In all analyzed lineages, the number of acquired new introns was substantially greater than the number of lost ancestral introns. This trend held even for lineages in which vertical evolution of genes involved more intron losses than gains, suggesting that gene duplication boosts intron insertion. However, dating gene duplications and the associated intron gains and losses based on the molecular clock assumption showed that very few, if any, introns were gained during the last ~100 million years of animal and plant evolution, in agreement with previous conclusions reached through analysis of orthologous gene sets. These results are generally compatible with the emerging notion of intensive insertion and loss of introns during transitional epochs in contrast to the relative quiet of the intervening evolutionary spans.     

A METHOD FOR TESTING THE CORRELATED EVOLUTION OF TWO BINARY CHARACTERS: ARE GAINS OR LOSSES CONCENTRATED ON CERTAIN BRANCHES OF A PHYLOGENETIC TREE?

A method is presented for assessing whether changes in a binary character are more concentrated than expected by chance on certain branches of a phylogenetic tree. It can be used to test for correlated evolution of two characters by asking whether changes in the first character are significantly concentrated on those branches on which the second character has a specified state. Thus, one could test whether this specified state is associated with, and thus might enable or select, gains or losses in the first character. The probability of achieving a concentration as or more extreme than that observed under the null hypotheses that changes are distributed randomly on the cladogram is obtained by calculating (a) the number of ways that n gains and m losses can be distributed on the cladogram and (b) the number of ways that p gains q losses can be distributed on the branches of interest given n gains and m losses in the cladogram overall. Summing (b) for appropriate p and q then dividing by (a) yields the desired probability. Simulations suggest that biases resulting from errors in parsimony reconstructions of ancestral states are not extreme.     

Phylogeny of shorebirds, gulls, and alcids (Aves: Charadrii) from the cytochrome-b gene: parsimony, Bayesian inference, minimum evolution, and quartet puzzling

Charadrii (shorebirds, gulls, and alcids) have exceptional diversity in ecological, behavioral, and life-history traits. A phylogenetic framework is necessary to fully understand the relationships among these traits. Despite several attempts to resolve the phylogeny of the Charadrii, none have comprehensively utilized molecular sequence data. Complete and partial cytochrome-b gene sequences for 86 Charadrii and five Falconides species (as outgroup taxa) were obtained from GenBank and aligned. We analyzed the resulting matrices using parsimony, Bayesian inference, minimum evolution, and quartet puzzling methods. Posterior probabilities, decay indices, and bootstrapping provide strong support for four major lineages consisting of gulls, alcids, plovers, and sandpipers, respectively. The broad structure of the trees differ significantly from all previous hypotheses of Charadrii phylogeny in placing the plovers at the base of the tree below the sandpipers in a pectinate sequence towards a large clade of gulls and alcids. The parsimony, Bayesian, and minimum evolution models provide strong evidence for this phylogenetic hypothesis. This is further corroborated by non-tree based measures of support and conflict (Lento plots). The quartet puzzling trees are poorly resolved and inconclusive.