Rare genomic changes as a tool for phylogenetics

Origins of primate chromosomes – as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences

This review examines recent advances in comparative eutherian cytogenetics, including Zoo-FISH data from 30 non-primate species. These data provide insights into the nature of karyotype evolution and enable the confident reconstruction of ancestral primate and boreo-eutherian karyotypes with diploid chromosome numbers of 48 and 46 chromosomes, respectively. Nine human autosomes (1, 5, 6, 9, 11, 13, 17, 18, and 20) represent the syntenies of ancestral boreo-eutherian chromosomes and have been conserved for about 95 million years. The average rate of chromosomal exchanges in eutherian evolution is estimated to about 1.9 rearrangements per 10 million years (involving 3.4 chromosome breaks). The integrated analysis of Zoo-FISH data and alignments of human and mouse draft genome sequences allow the identification of breakpoints involved in primate evolution. Thus, the boundaries of ancestral eutherian conserved segments can be delineated precisely. The mapping of rearrangements onto the phylogenetic tree visualizes landmark chromosome rearrangements, which might have been involved in cladogenesis in eutherian evolution.

Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase beta-subunit gene

Molecular investigations of deep-level relationships within and among the animal phyla have been hampered by a lack of slowly evolving genes that are amenable to study by molecular systematists. To provide new data for use in deep-level metazoan phylogenetic studies, primers were developed to amplify a 1.3-kb region of the alpha subunit of the nuclear-encoded sodium-potassium ATPase gene from 31 bilaterians representing several phyla. Maximum parsimony, maximum likelihood, and Bayesian analyses of these sequences (combined with ATPase sequences for 23 taxa downloaded from GenBank) yield congruent trees that corroborate recent findings based on analyses of other data sets (e.g., the 18S ribosomal RNA gene). The ATPase-based trees support monophyly for several clades (including Lophotrochozoa, a form of Ecdysozoa, Vertebrata, Mollusca, Bivalvia, Gastropoda, Arachnida, Hexapoda, Coleoptera, and Diptera) but do not support monophyly for Deuterostomia, Arthropoda, or Nemertea. Parametric bootstrapping tests reject monophyly for Arthropoda and Nemertea but are unable to reject deuterostome monophyly. Overall, the sodium-potassium ATPase alpha-subunit gene appears to be useful for deep-level studies of metazoan phylogeny.

Isolation and Molecular Evolution of the Selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) Genes in the Dog Family, Canidae

In an effort to identify rapidly evolving nuclear sequences useful for phylogenetic analyses of closely related species, we isolated two genes transcribed by RNA polymerase III (pol III), the selenocysteine tRNA gene (TRSP) and an RNase P RNA (RPPH1) gene from the domestic dog (Canis familiaris). We focus on genes transcribed by pol III because their coding regions are small (generally 100-300 base pairs [bp]) and their essential promoter elements are located within a couple of hundred bps upstream of the coding region. Therefore, we predicted that regions flanking the coding region and outside of the promoter elements would be free of constraint and would evolve rapidly. We amplified TRSP from 23 canids and RPPH1 from 12 canids and analyzed the molecular evolution of these genes and their utility as phylogenetic markers for resolving relationships among species in Canidae. We compared the rate of evolution of the gene-flanking regions to other noncoding regions of nuclear DNA (introns) and to the mitochondrial encoded COII gene. Alignment of TRSP from 23 canids revealed that regions directly adjacent to the coding region display high sequence variability. We discuss this pattern in terms of functional mechanisms of transcription. Although the flanking regions evolve no faster than introns, both genes were found to be useful phylogenetic markers, in part, because of the synapomorphic indels found in the flanking regions. Gene trees generated from the TRSP and RPPH1 loci were generally in agreement with the published mtDNA phylogeny and are the first phylogeny of Canidae based on nuclear sequences.

Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life

Effects of taxonomic sampling and conflicting signal on the inference of seed plant trees supported in previous molecular analyses were explored using 13 single-locus data sets. Changing the number of taxa in single-locus analyses had limited effects on log likelihood differences between the gnepine (Gnetales plus Pinaceae) and gnetifer (Gnetales plus conifers) trees. Distinguishing among these trees also was little affected by the use of different substitution parameters. The 13-locus combined data set was partitioned into nine classes based on substitution rates. Sites evolving at intermediate rates had the best likelihood and parsimony scores on gnepine trees, and those evolving at the fastest rates had the best parsimony scores on Gnetales-sister trees (Gnetales plus other seed plants). When the fastest evolving sites were excluded from parsimony analyses, well-supported gnepine trees were inferred from the combined data and from each genomic partition. When all sites were included, Gnetales-sister trees were inferred from the combined data, whereas a different tree was inferred from each genomic partition. Maximum likelihood trees from the combined data and from each genomic partition were well-supported gnepine trees. A preliminary stratigraphic test highlights the poor fit of Gnetales-sister trees to the fossil data.

Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora

Cross-species painting (fluorescence in situ hybridization) with 23 (human Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Chrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.

Phylogenetic Mapping of Intron Positions: A Case Study of Translation Initiation Factor eIF2γ

Eukaryotic translation initiation factor 2 (eIF2) is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed of three subunits, alpha, beta, and gamma. Subunit gamma shows the strongest conservation, and it confers both tRNA and GTP/GDP binding. Using intron positioning and protein sequence alignment, here we show that eIF2gamma is a suitable phylogenetic marker for eukaryotes. We determined or completed the sequences of 13 arthropod eIF2gamma genes. Analyzing the phylogenetic distribution of 52 different intron positions in 55 distantly related eIF2gamma genes, we identified ancient ones and shared derived introns in our data set. Obviously, intron positioning in eIF2gamma is evolutionarily conserved. However, there were episodes of complete and partial intron losses followed by intron gains. We identified 17 clusters of intron positions based on their distribution. The evolution of these clusters appears to be connected with preferred exon length and can be used to estimate the relative timing of intron gain because nearby precursor introns had to be erased from the gene before the new introns could be inserted. Moreover, we identified a putative case of intron sliding that constitutes a synapomorphic character state supporting monophyly of Coleoptera, Lepidoptera, and Diptera excluding Hymenoptera. We also performed tree reconstructions using the eIF2gamma protein sequences and intron positioning as phylogenetic information. Our results support the monophyly of Viridoplantae, Ascomycota, Homobasidiomyceta, and Apicomplexa.

Molecular Phylogenetic Analysis Places Percolomonas cosmopolites within Heterolobosea: Evolutionary Implications

Percolomonas cosmopolitus is a common free-living flagellate of uncertain phylogenetic position that was placed within the Heterolobosea on the basis of ultrastructure studies. To test the relationship between Percolomonas and Heterolobosea, we analysed the primary structure of the actin and small-subunit ribosomal RNA (SSU rRNA) genes of P. cosmopolitus as well as the predicted secondary structure of the SSU rRNA. Percolomonas shares common secondary structure patterns of the SSU rRNA with heterolobosean taxa, which, together with the results of actin gene analysis, confirms that it is closely related to Heterolobosea. Phylogenetic reconstructions based on the sequences of the SSU rRNA gene suggest Percolomonas belongs to the family Vahlkampfiidae. The first Bayesian analysis of a large taxon sampling of heterolobosean SSU rRNA genes clarifies the phylogenetic relationships within this group.

Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes

BACKGROUND

The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants. However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree.

RESULTS

Chloroplast DNA physical maps were constructed for eighteen representatives of the family. So many gene order changes have occurred among the genomes that characterizing individual mutational events was not always possible. Therefore, we examined different, novel scoring methods to prepare data matrices for cladistic analysis. These approaches yielded largely congruent results but varied in amounts of resolution and homoplasy. The strongly supported nodes were common to all gene order analyses as well as to parallel analyses based on ITS and rbcL sequence data. The results suggest some interesting and unexpected intrafamilial relationships. For example fifteen of the taxa form a derived clade; whereas the remaining three taxa--Platycodon, Codonopsis, and Cyananthus--form the basal clade. This major subdivision of the family corresponds to the distribution of pollen morphology characteristics but is not compatible with previous taxonomic treatments.

CONCLUSIONS

Our use of gene order data in the Campanulaceae provides the most highly resolved phylogeny as yet developed for a plant family using only cpDNA rearrangements. The gene order data showed markedly less homoplasy than sequence data for the same taxa but did not resolve quite as many nodes. The rearrangement characters, though relatively few in number, support robust and meaningful phylogenetic hypotheses and provide new insights into evolutionary relationships within the Campanulaceae.

Novel slc22 transporter homologs in fly, worm, and human clarify the phylogeny of organic anion and cation transporters

Slc22 family organic anion and cation transporters (OATs, OCTs, and OCTNs) are transmembrane proteins expressed predominantly in kidney and liver. These proteins mediate the uptake or excretion of numerous physiologically (and pharmacologically) important compounds, and accordingly have been the focus of intensive study. Here we investigate the molecular phylogeny of the slc22 transporters, identifying homologs in Drosophila and C. elegans, several of which are developmentally regulated, as well as reporting the cloning of a novel human family member, UST6, expressed exclusively in liver in both embryo and adult. The latter helps define a subfamily within the OATs, which appears to have human- and rodent-specific members, raising potential issues with respect to the use of rodents as models for the transport of organic anions (which include many pharmaceuticals) in humans. Although this phylogenetic inference could not be made on the basis of sequence alignment, analysis of intron phasing suggests that the OAT, OCT, and OCTN lineages of the slc22 family formed after the divergence of vertebrates and invertebrates. Subsequently, these lineages expanded through independent tandem duplications to produce multiple gene pairs. After analyzing over 200 other transporter genes, we find such pairing to be relatively specific to vertebrate organic anion and cation transporters, suggesting selection for gene pairing operating within this family in particular. This might reflect a requirement for redundancy or broader substrate specificity in vertebrates (compared to invertebrates), due to their greater physiological complexity and thus potentially broader exposure to organic ions.

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.

The multimeric beta-thymosin found in nematodes and arthropods is not a synapomorphy of the Ecdysozoa

The Ecdysozoa hypothesis proposes a clade of animals including arthropods and nematodes that share the characteristic of periodic molting or ecdysis. The original evidence supporting this hypothesis came from molecular phylogenies based on ribosomal RNA gene sequences. Contrary evidence has come from studies of multiple protein coding genes. One of the most convincing bits of supporting evidence for this theory has been the observation of an unusual multimeric form of the beta-thymosin gene in the genomes of Drosophila melanogaster and Caenorhabditis elegans where, in other metazoans that had been studied, a monomeric form has been found. Here I show that recently deposited sequence data reveal that the multimeric form is in fact a characteristic of all major subdivisions of the Metazoa. The multimeric form is present in a deuterostome, Ciona intestinalis, a lophotrochozoan, Hermissenda crassicornis, and in the ecdysozoans and also exists outside the Metazoa in a fungus. The presence of the multimeric form in nematodes and arthropods, therefore, although not contradicting the Ecdysozoa hypothesis, gives it no support. The absence of the monomeric form in the completely sequenced flies and nematodes may suggest they are linked but, lacking the complete genomes of other ecdysozoans, proving its total absence from the Ecdysozoa is not possible. Furthermore, the absence of the monomeric form from the genome of the deuterostome Ciona suggests that the absence of this character is an unreliable indicator of relationships.

Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis

Relative positions of nematodes, arthropods, and chordates in animal phylogeny remain uncertain. The traditional tree topology joins arthropods with chordates in a coelomate clade, whereas nematodes, which lack a coelome, occupy a basal position. However, the current leading hypothesis, based on phylogenetic trees for 18S ribosomal RNA and several proteins, joins nematodes with arthropods in a clade of molting animals, Ecdysozoa. We performed a phylogenetic analysis of over 500 sets of orthologous proteins, which are represented in plants, animals, and fungi, using maximum likelihood, maximum parsimony, and distance methods. Additionally, to increase the statistical power of topology tests, the same methods were applied to concatenated alignments of subunits of eight conserved macromolecular complexes. The majority of the methods, when applied to most of the orthologous clusters, both concatenated and individual, grouped the fly with humans to the exclusion of the nematode, in support of the coelomate phylogeny. Trees were also constructed using information on insertions and deletions in orthologous proteins, combinations of domains in multidomain proteins, and presence-absence of species in clusters of orthologs. All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss.

A phase transition for a random cluster model on phylogenetic trees

We investigate a simple model that generates random partitions of the leaf set of a tree. Of particular interest is the reconstruction question: what number k of independent samples (partitions) are required to correctly reconstruct the underlying tree (with high probability)? We demonstrate a phase transition for k as a function of the mutation rate, from logarithmic to polynomial dependence on the size of the tree. We also describe a simple polynomial-time tree reconstruction algorithm that applies in the logarithmic region. This model and the associated reconstruction questions are motivated by a Markov model for genomic evolution in molecular biology.

Molecular phylogeny of the Platyhelminthes

The phylum Platyhelminthes has traditionally been considered the most basal bilaterian taxon. The main difficulty with this placement is the lack of convincing synapomorphies for all Platyhelminthes, which suggest that they are polyphyletic. Recent molecular findings based on 18S rDNA sequence data and number and type of Hox genes strongly suggest that the majority of Platyhelminthes are members of the lophotrochozoan protostomes, whereas the Acoelomorpha (Acoela + Nemertodermatida) fall outside of the Platyhelminthes as the most basal bilaterian taxon. Here we review phylum-wide analyses based on complete ribosomal and other nuclear genes addressed to answer the main issues facing systematics and phylogeny of Platyhelminthes. We present and discuss (i) new corroborative evidence for the polyphyly of the Platyhelminthes and the basal position of Acoelomorpha; (ii) a new consensus internal tree of the phylum; (iii) the nature of the sister group to the Neodermata and the hypotheses on the origin of parasitism; and (iv) the internal phylogeny of some rhabditophoran orders. Some methodological caveats are also introduced. The need to erect a new phylum, the Acoelomorpha, separate from the Platyhelminthes (now Catenulida + Rhabditophora) and based on present and new morphological and molecular characters is highlighted, and a proposal made.

Chromosome painting in the African four-striped mouse Rhabdomys pumilio: detection of possible murid specific contiguous segment combinations

Fluorescence in-situ hybridization was used to construct a comparative chromosome map between the laboratory mouse, Mus musculus and the African four-striped mouse, Rhabdomys pumilio. A high degree of homology between the species was detected using both FISH and G-banding. Ten mouse chromosomes (2-4, 7, 14-16, 18, 19 and the X) were retained as chromosomal arms or intact chromosome blocks. Six mouse chromosome painting probes that correspond to mouse autosomes 5, 6, 8, 11, 12 and 13, produced double signals; the remaining four painting probes (1, 9, 10 and 17) hybridized to three or more R. pumilio chromosomes respectively. In total, the 20 mouse chromosome paints revealed 40 segments of conserved synteny in the R. pumilio genome. Most of the mouse chromosomes that produced single signals in R. pumilio have previously been shown to be conserved in the Black and Norwegian rats and the Chinese hamster. Eight contiguous segment associations appear to be R. pumilio specific, two were shared by R. pumilio and the Black and Norwegian rats, but to the exclusion of the Chinese hamster. Our data suggest that mouse chromosomes 1, 10, and 17 have undergone extensive rearrangements during genome evolution in the murids and may be useful markers for enhancing our understanding of the mode and tempo of chromosome evolution in rodents.

Chromosomal phylogeny and evolution of gibbons (Hylobatidae)

Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to be picked up.

Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree

Despite the availability of large molecular data sets, the position of the root of the eutherian tree remains a controversial issue. Depending on source data, taxon sampling and analytical approach, the root can be placed at either Afrotheria, Xenarthra, Afrotheria+Xenarthra, or murid rodents. We explored the phylogenetic potential of indels in four nuclear protein-coding genes (SCA1, PRNP, TNFalpha, and HspB3) with regard to a possible rooting at the murid branch. According to parsimony principles, five indels were interpreted to contradict such a rooting, and one indel to support it. The results illustrate that indels, despite the occurrence of homoplasy, can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.

The phylogeny of howler monkeys (Alouatta, Platyrrhini): reconstruction by multicolor cross-species chromosome painting

We performed multidirectional chromosome painting in a comparative cytogenetic study of the three howler monkey species Alouatta fusca, A. caraya and A. seniculus macconnelli (Atelinae, Platyrrhini) in order to reconstruct phylogenetic relationships within this genus. Comparative genome maps between these species were established by multicolor fluorescence in-situ hybridization (FISH) employing human, Saguinus oedipus and Lagothrix lagothricha chromosome-specific probes. The three species included in this study and previously analyzed howler monkey species were subjected to a phylogenetic analysis on the basis of a data matrix comprised of 98 discrete molecular cytogenetic characters. The results revealed that howler monkeys represent the genus with the most extensive karyotype diversity within Platyrrhini so far analyzed with high levels of intraspecific chromosomal variability. Two different multiple sex chromosome systems were identified. The phylogenetic analysis indicated that Alouatta is a monophyletic clade which can be derived from a proposed ancestral Atelinae karyotype of 2n = 62 chromosomes by a chromosome fusion, a fission, a Y-autosomal translocation and a pericentric inversion. Following these suggestions, the genus Alouatta can be divided into two distinct species groups: the first includes A. caraya and A. belzebul, the second A. s. macconnelli, A. sara, A. s. arctoidea and A. fusca.

Conflicting phylogenetic signals at the base of the metazoan tree

A phylogenetic framework is essential for under-standing the origin and evolution of metazoan development. Despite a number of recent molecular studies and a rich fossil record of sponges and cnidarians, the evolutionary relationships of the early branching metazoan groups to each other and to a putative outgroup, the choanoflagellates, remain uncertain. This situation may be the result of the limited amount of phylogenetic information found in single genes and the small number of relevant taxa surveyed. To alleviate the effect of these analytical factors in the phylogenetic recons-truction of early branching metazoan lineages, we cloned multiple protein-coding genes from two choanoflagellates and diverse sponges, cnidarians, and a ctenophore. Comparisons of sequences for alpha-tubulin, beta-tubulin, elongation factor 2, HSP90, and HSP70 robustly support the hypothesis that choanoflagellates are closely affiliated with animals. However, analyses of single and concatenated amino acid sequences fail to resolve the relationships either between early branching metazoan groups or between Metazoa and choano-flagellates. We demonstrate that variable rates of evolution among lineages, sensitivity of the analyses to taxon selection, and conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences. A consensus view of animal evolution may require investigations of genome-scale characters.

A comparative ZOO-FISH analysis in bats elucidates the phylogenetic relationships between Megachiroptera and five microchiropteran families

Fluorescence in-situ hybridization with human whole chromosome painting probes (WCPs) was applied to compare the karyotypes of members of five bat families. Twenty-five evolutionarily conserved units (ECUs) were identified by ZOO-FISH analysis. In 10 of these 25 ECUs, thorough GTG-band comparison revealed an identical banding pattern in all families studied. Differences in the remaining ECUs were used as characters to judge the phylogenetic relationships within Chiroptera. Close relationships were found between Rhinolophidae and Hipposideridae. Also closely related are the representatives of the yangochiropteran families Phyllostomidae (genus studied: Glossophaga, Volleth et al. 1999), Molossidae and Vespertilionidae. All microchiropteran species studied here share four common features not found in the megachiropteran species Eonycteris spelaea. Two of these are considered as derived characters with a high probability of parallel evolution. On the other hand, Eonycteris shares one common, probably derived feature with the rhinolophoid families Rhinolophidae and Hipposideridae and an additional one only with Hipposideridae. At the moment, the relationships between Yangochiroptera, Rhinolophoidea and Megachiroptera must be left in an unsolved trichotomy. Comparison of neighboring segment combinations found in Chiroptera with those found in other mammalian taxa revealed six synapomorphic features for Chiroptera. Therefore, for karyological reasons, monophyly of Chiroptera is strongly supported.

Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus)

To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon and intron sequences of long-wavelength rhodopsin (LW Rh), arginine kinase (ArgK), and elongation factor-1alpha (EF-1alpha) F2 copy genes. LW Rh intron had only a few uninformative gaps, ArgK intron had relatively long gaps that were easily aligned, and EF-1alpha intron had many short gaps, resulting in multiple optimal alignments. The unambiguously aligned gaps within ArgK intron sequences showed no homoplasy upon the substitution-based tree, and phylogenetic signals within ambiguously aligned regions of EF-1alpha intron were highly congruent with those of base substitutions. We further analyzed the contribution of gap characters to phylogenetic reconstruction by incorporating them in parsimony analysis. Inclusion of gap characters consistently improved support for nodes recovered by substitutions, and inclusion of ambiguously aligned regions of EF-1alpha intron resolved several additional nodes, most of which were apical on the phylogeny. We conclude that gaps are an exceptionally reliable source of phylogenetic information that can be used to corroborate and refine phylogenies hypothesized by base substitutions, at least at lower taxonomic levels. At present, full use of gaps in phylogenetic reconstruction is best achieved in parsimony analysis, pending development of well-justified and generally applicable methods for incorporating indels in explicitly model-based methods.

Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data

Oak gallwasps are cyclically parthenogenetic insects that induce a wide diversity of highly complex species- and generation-specific galls on oaks and other Fagaceae. Phylogenetic relationships within oak gallwasps remain to be established, while sexual and parthenogenetic generations of many species remain unpaired. Previous work on oak gallwasps has revealed substantial intra-specific variation, particularly between regions known to represent discrete Pleistocene glacial refuges. Here we use statistical phylogenetic inference methods on sequence data for a fragment of the mitochondrial cytochrome b gene to reconstruct the relationships among 62 oak gallwasp species. For 16 of these we also include 23 additional cytochrome b haplotype sequences from different Pleistocene refuge areas to test the effect of intra-specific variation on inter-specific phylogeny reconstruction. The reconstructed phylogenies show good intra-generic resolution and identify several conserved clades, but fail to reconstruct either very recent or very ancient divergences. Nine of the 16 species represented by multiple haplotypes are not monophyletic. The apparent discordance between the recovered gene tree and the current taxonomic classification can be explained through: (a) collapsing of some species currently known only from either a sexual or a parthenogenetic generation into a single cyclically parthenogenetic entity; (b) sorting of ancestral polymorphism in diverging lineages, and (c) horizontal transfer of haplotypes, perhaps due to hybridization within glacial refuges. Our conclusions emphasise the need for careful intra-specific sampling when reconstructing phylogenies for radiations of closely related species and imply that for certain taxonomic groups full phylogenetic resolution (using molecular markers) may not be attainable.

Molecular evolution of the mammalian alpha 2B adrenergic receptor

The alpha 2B adrenergic receptor (A2AB) is a heptahelical G protein-coupled receptor for catecholamines. We compared the almost complete coding region (about 1,175 bp) of the A2AB gene from 48 mammalian species, including eight newly determined sequences, representing all the 18 eutherian and two marsupial orders. Comparison of the encoded proteins reveals that residues thought to be involved in agonist binding are highly conserved, as are the regions playing a role in G protein-coupling. The three extracellular loops are generally more variable than the transmembrane domains and two of the intracellular loops, indicating a lower functional constraint. However, the greatest variation is observed in the very long, third intracellular loop, where only a few residues and a polyglutamyl tract are preserved. Although this polyglutamyl domain displays a great variation in length, its presence in all described A2ABs confirms its proposed role in agonist-dependent phosphorylation of the third intracellular loop. Phylogenetic analyses of the A2AB data set, including Bayesian methods, recognized the superordinal clades Afrotheria, Laurasiatheria, and Euarchontoglires, in agreement with recent molecular evidence, albeit with lower support. Within Afrotheria, A2AB strongly supports the paenungulate clade and the association of the continental African otter shrew with Malagasy tenrecs. Among Laurasiatheria, A2AB confirms the nesting of whales within the artiodactyls, as a sister group to hippopotamus. Within the Euarchontoglires, there is constant support for rodent monophyly.

A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny

Although data are available from only vertebrates, urochordates, and three nonchordate animals, there are definite differences in the structures of classic cadherins between vertebrates plus urochordates and nonchordates. In this study we examined structural diversity of classic cadherins among bilaterian animals by obtaining new data from an amphioxus (Cephalochordata, Chordata), an acorn worm (Hemichordata), a sea star (Echinodermata), and an oyster (Mollusca). The structures of newly identified nonchordate cadherins are grouped together with those of the known sea urchin and Drosophila cadherins, whereas the structure of an amphioxus (Branchiostoma belcheri) cadherin, designated BbC, is differently categorized from those of other known chordate cadherins. BbC is identified as a cadherin by its cytoplasmic domain whose sequence is highly related to the cytoplasmic sequences of all known classic cadherins, but it lacks all of the five repeats constituting the extracellular homophilic-binding domain of other chordate cadherins. The ectodomains of BbC match the ectodomains found in nonchordate cadherins but not present in other chordate cadherins. We show that the BbC functions as a cell-cell adhesion molecule when expressed in Drosophila S2 cells and localizes to adherens junctions in the ectodermal epithelia in amphioxus embryos. We argue that BbC is the amphioxus homologue of the classic cadherins involved in the formation of epithelial adherens junctions. The structural relationships of the cadherin molecules allow us to propose a possibility that cephalochordates might be basal to the sister-groups vertebrates and urochordates.

The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout

Technical and biological hurdles have precluded the retrieval of nuclear gene genealogies within most species. Among these obstacles, the possibility of intragenic recombination is one of the most demanding challenges. We studied the utility of nuclear genes for intraspecific evolutionary inferences by selecting a nuclear gene that exhibits patterns of considerable geographic differentiation in the brown trout (Salmo trutta) species complex. Haplotype variation from a nucleotide sequence of approximately 3.7 kb encompassing a portion of the transferrin (TF) gene was surveyed in 31 brown trout individuals collected across the native Eurasian range. Statistically significant recombination and gene conversion events were detected. However, we showed that the substantial cladistic structure was not disrupted by recombination or gene conversion events and the additional structure was estimated to have emerged after those events. Because loci with unusually high levels of variation might indicate the presence of selection, we tested the hypothesis of neutrality and found some evidence for directional selection. The strong geographic signal observed in the TF genealogy, coupled with the current spatial distribution of electromorphs, gave us the ability to draw empirical phylogeographic inferences. We delineated the composition of current brown trout populations on the basis of 3,625 individuals electrophoretically scored for the TF locus. We hypothesized scenarios of historical radiation and dispersal events, thus providing new insights refining previous allozyme and mtDNA inferences. We infer that the most ancestral brown trout populations inhabited tributaries from the Black, Caspian, and Aral Sea drainages. An early radiation of the species occurred throughout the Mediterranean, followed by independent dispersal events from the Adriatic to the southernmost Iberian Atlantic and, more recently, a rapid expansion throughout most of the Atlantic drainages.

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.

Archaeal phylogeny based on ribosomal proteins

Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in most of the archaeal species. This phylogeny was remarkably congruent with the rRNA phylogeny, suggesting that both reflected the actual phylogeny of the domain Archaea even if some nodes remained unresolved. In both cases, the branches leading to hyperthermophilic species were short, suggesting that the evolutionary rate of their genes has been slowed down by structural constraints related to environmental adaptation. In addition, to estimate the impact of lateral gene transfer (LGT) on our tree reconstruction, we used a new method that revealed that 8 genes out of the 53 ribosomal proteins used in our study were likely affected by LGT. This strongly suggested that a core of 45 nontransferred ribosomal protein genes existed in Archaea that can be tentatively used to infer the phylogeny of this domain. Interestingly, the tree obtained using only the eight ribosomal proteins likely affected by LGT was not very different from the consensus tree, indicating that LGT mainly brought random phylogenetic noise. The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity.

Evolutionary relationships among self-incompatibility RNases

T2-type RNases are responsible for self-pollen recognition and rejection in three distantly related families of flowering plants-the Solanaceae, Scrophulariaceae, and Rosaceae. We used phylogenetic analyses of 67 T2-type RNases together with information on intron number and position to determine whether the use of RNases for self-incompatibility in these families is homologous or convergent. All methods of phylogenetic reconstruction as well as patterns of variation in intron structure find that all self-incompatibility RNases along with non-S genes from only two taxa form a monophyletic clade. Several lines of evidence suggest that the best interpretation of this pattern is homology of self-incompatibility RNases from the Scrophulariaceae, Solanaceae, and Rosaceae. Because the most recent common ancestor of these three families is the ancestor of approximately 75% of dicot families, our results indicate that RNase-based self-incompatibility was the ancestral state in the majority of dicots.

The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny

The second intron in the mitochondrial gene nad1 was surveyed using PCR, DNA sequencing, or Southern hybridization in 323 species (313 genera, 212 families) of seed plants. The intron was absent in all 22 species (22 genera, 8 families) of non-Pinaceae conifers studied, in Welwitschia mirabilis, and in seven angiosperms. Whereas absence of the intron in seven angiosperms and Welwitschia is likely due to seven independent losses when evaluated against the recently published multigene phylogenies, the lack of the intron in all non-Pinaceae conifers can be best explained by a single loss. These data suggest that the non-Pinaceae conifers represent a monophyletic group. We also conducted a phylogenetic analysis of seed plants using a combined data set of the partial exon and intron sequences of nad1 generated from this study and published sequences of mitochondrial cox1 and small subunit (SSU) rDNA, chloroplast rbcL, and nuclear 18S rDNA. The results supported the split of conifers into two groups: Pinaceae and non-Pinaceae conifers. The Gnetales were sister to Pinaceae, in agreement with the conclusion from other recent molecular phylogenetic studies that refute the anthophyte hypothesis.

Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution?

The evolutionary significance of introns remains a mystery. The current availability of several complete eukaryotic genomes permits new studies to probe the possible function of these peculiar genomic features. Here we investigate the degree to which gene structure (intron position, phase and length) is conserved between homologous protein domains. We find that for certain extracellular-signalling and nuclear domains, gene structures are similar even when protein sequence similarity is low or not significant and sequences can only be aligned with a knowledge of protein tertiary structure. In contrast, other domains, including most intracellular signalling modules, show little gene structure conservation. Intriguingly, many domains with conserved gene structures, such as cytokines, are involved in similar biological processes, such as the immune response. This suggests that gene structure conservation may be a record of key events in evolution, such as the origin of the vertebrate immune system or the duplication of nuclear receptors in nematodes. The results suggest ways to detect new and potentially very remote homologues, and to construct phylogenies for proteins with limited sequence similarity.

Use of whole genome sequence data to infer baculovirus phylogeny

Several phylogenetic methods based on whole genome sequence data were evaluated using data from nine complete baculovirus genomes. The utility of three independent character sets was assessed. The first data set comprised the sequences of the 63 genes common to these viruses. The second set of characters was based on gene order, and phylogenies were inferred using both breakpoint distance analysis and a novel method developed here, termed neighbor pair analysis. The third set recorded gene content by scoring gene presence or absence in each genome. All three data sets yielded phylogenies supporting the separation of the Nucleopolyhedrovirus (NPV) and Granulovirus (GV) genera, the division of the NPVs into groups I and II, and species relationships within group I NPVs. Generation of phylogenies based on the combined sequences of all 63 shared genes proved to be the most effective approach to resolving the relationships among the group II NPVs and the GVs. The history of gene acquisitions and losses that have accompanied baculovirus diversification was visualized by mapping the gene content data onto the phylogenetic tree. This analysis highlighted the fluid nature of baculovirus genomes, with evidence of frequent genome rearrangements and multiple gene content changes during their evolution. Of more than 416 genes identified in the genomes analyzed, only 63 are present in all nine genomes, and 200 genes are found only in a single genome. Despite this fluidity, the whole genome-based methods we describe are sufficiently powerful to recover the underlying phylogeny of the viruses.