A web-database of mammalian morphology and a reanalysis of placental phylogeny

Background  

Recent publications concerning the interordinal phylogeny of placental mammals have converged on a common signal, consisting of four major radiations with some ambiguity regarding the placental root. The DNA data with which these relationships have been reconstructed are easily accessible from public databases; access to morphological characters is much more difficult. Here, I present a graphical web-database of morphological characters focusing on placental mammals, in tandem with a combined-data phylogenetic analysis of placental mammal phylogeny.     

Ancestral state reconstruction reveals multiple independent evolution of diagnostic morphological characters in the "Higher Oribatida" (Acari), conflicting with current classification schemes

Background  

The use of molecular genetic data in phylogenetic systematics has revolutionized this field of research in that several taxonomic groupings defined by traditional taxonomic approaches have been rejected by molecular data. The taxonomic classification of the oribatid mite group Circumdehiscentiae ("Higher Oribatida") is largely based on morphological characters and several different classification schemes, all based upon the validity of diagnostic morphological characters, have been proposed by various authors. The aims of this study were to test the appropriateness of the current taxonomic classification schemes for the Circumdehiscentiae and to trace the evolution of the main diagnostic traits (the four nymphal traits scalps, centrodorsal setae, sclerits and wrinkled cuticle plus octotaxic system and pteromorphs both in adults) on the basis of a molecular phylogenetic hypothesis by means of parsimony, likelihood and Bayesian approaches.     

Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data

Background  

Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria.     

Molecular phylogeny of pearl oysters and their relatives (Mollusca,Bivalvia, Pterioidea)

Background  

The superfamily Pterioidea is a morphologically and ecologically diverse lineage of epifaunal marine bivalves distributed throughout the tropical and subtropical continental shelf regions. This group includes commercially important pearl culture species and model organisms used for medical studies of biomineralization. Recent morphological treatment of selected pterioideans and molecular phylogenetic analyses of higher-level relationships in Bivalvia have challenged the traditional view that pterioidean families are monophyletic. This issue is examined here in light of molecular data sets composed of DNA sequences for nuclear and mitochondrial loci, and a published character data set of anatomical and shell morphological characters.     

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

Background  

Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution.     

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

We present a mitochondrial (mt) genome phylogeny inferring relationships within Neuropterida (lacewings, alderflies and camel flies) and between Neuropterida and other holometabolous insect orders. Whole mt genomes were sequenced for Sialis hamata (Megaloptera: Sialidae), Ditaxis latistyla (Neuroptera: Mantispidae), Mongoloraphidia harmandi (Raphidioptera: Raphidiidae), Macrogyrus oblongus (Coleoptera: Gyrinidae), Rhopaea magnicornis (Coleoptera: Scarabaeidae), and Mordella atrata (Coleoptera: Mordellidae) and compared against representatives of other holometabolous orders in phylogenetic analyses. Additionally, we test the sensitivity of phylogenetic inferences to four analytical approaches: inclusion vs. exclusion of RNA genes, manual vs. algorithmic alignments, arbitrary vs. algorithmic approaches to excluding variable gene regions and how each approach interacts with phylogenetic inference methods (parsimony vs. Bayesian inference). Of these factors, phylogenetic inference method had the most influence on interordinal relationships. Bayesian analyses inferred topologies largely congruent with morphologically‐based hypotheses of neuropterid relationships, a monophyletic Neuropterida whose sister group is Coleoptera. In contrast, parsimony analyses failed to support a monophyletic Neuropterida as Raphidioptera was the sister group of the entire Holometabola excluding Hymenoptera, and Neuroptera + Megaloptera is the sister group of Diptera, a relationship which has not previously been proposed based on either molecular or morphological data sets. These differences between analytical methods are due to the high among site rate heterogeneity found in insect mt genomes which is properly modelled by Bayesian methods but results in artifactual relationships under parsimony. Properly analysed, the mt genomic data set presented here is among the first molecular data to support traditional, morphology‐based interpretations of relationships between the three neuropterid orders and their grouping with Coleoptera.     

Phylogenetic assessment of molecular and morphological data for eutherian mammals

The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequences and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests, which were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., > or = 95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla (Artiodactyla and Cetacea) and Paenungulata (Hyracoidea, Proboscidea, and Sirenia). In turn, some reasonable to strong evidence (> or = 85%) was obtained for Hyracoidea with Sirenia, Dermoptera with Scandentia, Glires (Lagomorpha with Rodentia), and Afrotheria (Amblysomus, Macroscelidea, Paenungulata, and Tubulidentata). Otherwise, no other interordinal clades were supported at these reasonable to strong levels. This overall lack of resolution for eutherian interordinal clusters agrees with other studies that suggest further progress will continue to be slow and difficult. Further resolution will require the integration of more recently published data, the continued sampling of taxa and characters, and the use of more powerful methods of data analysis.     

A multi gene sequence-based phylogeny of the Musaceae (banana) family

Background  

The classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.     

Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise

Background  

Hieracium s.str. is a complex species-rich group of perennial herbs composed of few sexual diploids and numerous apomictic polyploids. The existence of reticulation and the near-continuity of morphological characters across taxa seriously affect species determination, making Hieracium one of the best examples of a 'botanist's nightmare'. Consequently, its species relationships have not previously been addressed by molecular methods. Concentrating on the supposed major evolutionary units, we used nuclear ribosomal (ETS) and chloroplast (trnT - trnL) sequences in order to disentangle the phylogenetic relationships and to infer the origins of the polyploids.     

iGTP: A software package for large-scale gene tree parsimony analysis

Background  

The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.     

A New Baurusuchid (Crocodyliformes, Mesoeucrocodylia) from the Late Cretaceous of Brazil and the Phylogeny of Baurusuchidae

Background

Baurusuchidae is a group of extinct Crocodyliformes with peculiar, dog-faced skulls, hypertrophied canines, and terrestrial, cursorial limb morphologies. Their importance for crocodyliform evolution and biogeography is widely recognized, and many new taxa have been recently described. In most phylogenetic analyses of Mesoeucrocodylia, the entire clade is represented only by Baurusuchus pachecoi, and no work has attempted to study the internal relationships of the group or diagnose the clade and its members.

Methodology/Principal Findings

Based on a nearly complete skull and a referred partial skull and lower jaw, we describe a new baurusuchid from the Vale do Rio do Peixe Formation (Bauru Group), Late Cretaceous of Brazil. The taxon is diagnosed by a suite of characters that include: four maxillary teeth, supratemporal fenestra with equally developed medial and anterior rims, four laterally visible quadrate fenestrae, lateral Eustachian foramina larger than medial Eustachian foramen, deep depression on the dorsal surface of pterygoid wing. The new taxon was compared to all other baurusuchids and their internal relationships were examined based on the maximum parsimony analysis of a discrete morphological data matrix.

Conclusion

The monophyly of Baurusuchidae is supported by a large number of unique characters implying an equally large morphological gap between the clade and its immediate outgroups. A complex phylogeny of baurusuchids was recovered. The internal branch pattern suggests two main lineages, one with a relatively broad geographical range between Argentina and Brazil (Pissarrachampsinae), which includes the new taxon, and an endemic clade of the Bauru Group in Brazil (Baurusuchinae).     

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Background  

Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold.     

Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins

Background

The family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but these studies have included only a fraction of the extant diversity (a maximum of 26 out of the 46 currently recognized genera) and have failed to resolve deep relationships among internal clades. Here we readdress the systematics of pteropodids by applying a strategy to try to resolve ancient relationships within Pteropodidae, while providing further insight into subgroup membership, by 1) increasing the taxonomic sample to 42 genera; 2) increasing the number of characters (to >8,000 bp) and nuclear genomic representation; 3) minimizing missing data; 4) controlling for sequence bias; and 5) using appropriate data partitioning and models of sequence evolution.

Results

Our analyses recovered six principal clades and one additional independent lineage (consisting of a single genus) within Pteropodidae. Reciprocal monophyly of these groups was highly supported and generally congruent among the different methods and datasets used. Likewise, most relationships within these principal clades were well resolved and statistically supported. Relationships among the 7 principal groups, however, were poorly supported in all analyses. This result could not be explained by any detectable systematic bias in the data or incongruence among loci. The SOWH test confirmed that basal branches' lengths were not different from zero, which points to closely-spaced cladogenesis as the most likely explanation for the poor resolution of the deep pteropodid relationships. Simulations suggest that an increase in the amount of sequence data is likely to solve this problem.

Conclusions

The phylogenetic hypothesis generated here provides a robust framework for a revised cladistic classification of Pteropodidae into subfamilies and tribes and will greatly contribute to the understanding of character evolution and biogeography of pteropodids. The inability of our data to resolve the deepest relationships of the major pteropodid lineages suggests an explosive diversification soon after origin of the crown pteropodids. Several characteristics of pteropodids are consistent with this conclusion, including high species diversity, great morphological diversity, and presence of key innovations in relation to their sister group.     

SIMMAP: Stochastic character mapping of discrete traits on phylogenies

Background  

Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny.     

Organellar genomes of the four-toothed moss,Tetraphis pellucida

Background

Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.

Results

Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).

Conclusions

Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.     

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences,mitochondrial COI sequence,and morphological characters

Background  

Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera) using 69 species.     

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

Background  

Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allows missing characters. We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al.     

Are we degenerate tetraploids? More genomes,new facts

Background  

Within the bilaterians, the appearance and evolution of vertebrates is accompanied by enormous changes in anatomical, morphological and developmental features. This evolution of increased complexity has been associated with two genome duplications (2R hypothesis) at the origin of vertebrates. However, in spite of extensive debate the validity of the 2R hypothesis remains controversial. The paucity of sequence data in early years of genomic era was an intrinsic obstacle in tracking the genome evolutionary history of chordates.     

On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

Background  

Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems.