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PubMed2006

Evolution and diversification of the forest and hypogean ground-beetle genus Trechus in the Canary Islands.

The beetle genus Trechus (Carabidae) is represented in the Macaronesian Islands by 43 endemic species. The Canary Islands have 16 endemic species, with two adapted to hypogean life. Phylogenetic relationships among 177 individuals of 38 Canarian, Madeiran, Azorean and continental Trechus species were examined using mitochondrial DNA and nuclear internal transcribed spacer 2 (ITS2) sequence data. Results show two main lineages in the Canaries: one comprising two sister groups with species from the laurel forest of La Gomera and Tenerife, and the other containing the single species from Gran Canaria and a species complex in the four western islands including two troglobites. Calibrations were applied to a linearized tree using a relaxed molecular clock method to estimate the major evolutionary divergence times of the Canarian Trechus species. Although the species assemblage in this archipelago is relatively ancient (7-8 million years), much of the species diversity is recent. Transition to the hypogean environment is more consistent with the "adaptive shift" rather than with the competing "climatic relict" hypothesis.

Animals↗
PubMed2001

A new theory of phylogeny inference through construction of multidimensional vector space.

Here, a new theory of molecular phylogeny is developed in a multidimensional vector space (MVS). The molecular evolution is represented as a successive splitting of branch vectors in the MVS. The end points of these vectors are the extant species and indicate the specific directions reflected by their individual histories of evolution in the past. This representation makes it possible to infer the phylogeny (evolutionary histories) from the spatial positions of the end points. Search vectors are introduced to draw out the groups of species distributed around them. These groups are classified according to the nearby order of branches with them. A law of physics is applied to determine the species positions in the MVS. The species are regarded as the particles moving in time according to the equation of motion, finally falling into the lowest-energy state in spite of their randomly distributed initial condition. This falling into the ground state results in the construction of an MVS in which the relative distances between two particles are equal to the substitution distances. The species positions are obtained prior to the phylogeny inference. Therefore, as the number of species increases, the species vectors can be more specific in an MVS of a larger size, such that the vector analysis gives a more stable and reliable topology. The efficacy of the present method was examined by using computer simulations of molecular evolution in which all the branch- and end-point sequences of the trees are known in advance. In the phylogeny inference from the end points with 100 multiple data sets, the present method consistently reconstructed the correct topologies, in contrast to standard methods. In applications to 185 vertebrates in the alpha-hemoglobin, the vector analysis drew out the two lineage groups of birds and mammals. A core member of the mammalian radiation appeared at the base of the mammalian lineage. Squamates were isolated from the bird lineage to compose the outgroup, while the other living reptilians were directly coupled with birds without forming any sister groups. This result is in contrast to the morphological phylogeny and is also different from those of recent molecular analyses.

Amino Acid Sequence↗
PubMed1996

The phylogeny of Methanopyrus kandleri.

The phylogenetic position of Methanopyrus kandleri has been difficult to determine because reconstructions of phylogenetic trees based on rRNA sequences have been ambiguous. The most probable trees determined by most algorithms place the genus Methanopyrus at the base of a group that includes the halobacteria and the methanogens and their relatives, although occasionally some algorithms place this genus near the eocytes (the hyperthermophilic, sulfur-metabolizing prokaryotes), suggesting that it may belong to this lineage. In order to resolve the phylogeny of the genus Methanopyrus, we determined the sequence of an informative region of elongation factor 1-alpha that contains an 11-amino-acid insertion in eocytes and eukaryotes which is replaced by a 4-amino-acid insertion in methanogens, halobacteria, and eubacteria. On the basis of the results of our elongation factor 1-alpha gene analysis, we concluded that the genus Methanopyrus diverged from the eocyte branch before the eukaryotic and eocyte lineages separated and therefore is not an eocyte.

Amino Acid Sequence↗
PubMed2025

Homoploid Hybrid Speciation in a Marine Pelagic Fish.

Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process where new species arise through hybridisation of divergent lineages without changes in chromosome number. Although increasingly documented in various taxa and ecosystems, convincing cases of HHS in marine fishes have been lacking. This study presents a possible case of HHS in a pelagic marine fish based on comprehensive genomic, morphological, and ecological analyses. Population genomics, species tree estimation, and tests of introgression and admixture identified three sympatric clusters in Megalaspis cordyla in the western Pacific and the admixed nature of one cluster between the others. Moreover, model-based demographic inference favoured a hybrid speciation scenario over introgression for the origin of the admixed cluster. While contemporary gene flow suggested partial reproductive isolation, examination of occurrence data and ecologically relevant morphological characters suggested ecological differences between the clusters, potentially contributing to the reproductive isolation and niche partitioning in sympatry. The clusters are also morphologically distinguishable and thus can be taxonomically recognised as separate species. The hybrid cluster is restricted to the coasts of Taiwan and Japan, where all three clusters coexist. The parental clusters are additionally found in lower latitudes, where they display non-overlapping distributions. Given the geographical distributions, estimated times of species formation, and patterns of historical demographic changes, we propose that the Pleistocene glacial cycles were the primary driver of HHS in this system. We also develop an ecogeographic model of HHS in marine coastal ecosystems, including a novel hypothesis to explain the initial stages of HHS.

Animals↗
PubMed1995

Strain evolution in Caenorhabditis elegans: transposable elements as markers of interstrain evolutionary history.

Evolutionary relationships across taxa can be deduced from sequence divergence of proteins, RNA, or DNA; sequences which diverge rapidly, such as those of mitochondrial genes, have been especially useful for comparisons of closely related species, and--within limits--of strains within a species. We have utilized the transposable element Tc1 as a polymorphic marker to evaluate the evolutionary relationships among nine Caenorhabditis elegans strains. For five low-Tc1-copy strains, we compared patterns of restriction fragments hybridizing to a cloned Tc1 probe. Twenty of the 40 Tc1 insertion sites thus characterized were common to all five strains, and so presumably preceded strain divergence; the 20 differential bands were used to construct a maximum-parsimony tree relating these strains. In four high-copy-number stocks (three wild-type strains and a subline), we determined occupancy of 35 individual Tc1 insertion sites by a polymerase chain reaction assay. Surprisingly, the high-copy strains share a common subset of these Tc1 insertions, and the chromosomal distribution of conserved Tc1 sites is "clustered" with respect to the other elements tested. These data imply a close evolutionary relationship among the high-copy strains, such that two of these strains appear to have been derived from the highest-copy-number lineage (represented by two stocks) through crossing with a low-Tc1 strain. Abundances of Tc1 elements were also estimated for the four high-copy-number stocks, at approximately 200-500 copies per haploid genome, by quantitative dot-blot hybridization relative to two low-copy strains. Annealing with 32P-labeled probes corresponding to full-length Tc1, an oligonucleotide within the Tc1 terminal inverted repeats, and an internal Tc1 oligonucleotide, gave essentially identical results--indicating that Tc1 termini exist in the genome primarily as components of full-length Tc1 elements. A composite evolutionary tree is proposed, based on the locations and numbers of Tc1 elements in these strains, which is consistent with a four-branch intraspecific tree deduced previously by maximum-parsimony analyses of mitochondrial sequence changes; it also serves to elucidate the evolutionary history of transposon mobility.

Animals↗
PubMed1999

Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae).

Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north-south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.

Cell Nucleus↗
PubMed2000

Rapidly evolving lineages impede the resolution of phylogenetic relationships among Clitellata (Annelida).

The phylogenetic relationships of the Clitellata were investigated using a data set with published and new complete or partial 18S rRNA and mtCOI gene sequences of 13 and 49 taxa representing 8 and 14 families, respectively. Three different alignments were considered for 18S, and the possible influence of departures from rate constancy among sites was evaluated by analyses using a Gamma model of rate heterogeneity. Maximum-likelihood estimates of the shape parameter alpha of the Gamma distribution were very low, whatever the alignment or the gene considered, suggesting that phylogenetic reconstructions taking into account the rate heterogeneity among sites are likely to be the most reliable. Analyzed separately, the two genes did not resolve the relationships among the Clitellata, but the consensus tree was congruent with the morphology-based relationships. Our data suggest the inclusion of the Euhirudinea, Acanthobdellida, and Branchiobdellida in the Oligochaeta and suggest the Lumbriculidae as the link between both assemblages. Although separate analyses of both genes, as well as different alignments for the 18S rRNA sequences, yielded conflicting results concerning the phylogenetic position of leeches and leech-like worms vis-à-vis the Oligochaeta, subsequent analyses using the Gamma model greatly reduced the observed inconsistencies. Our analyses show that among the Clitellata, the leeches and the leech-like and gutless worms represent significantly faster evolving lineages. It is suggested that the observed higher mutation rates may be explained by the fact that these lineages contain almost exclusively commensal and/or parasitic taxa.

Animals↗
PubMed1996

Phylogenetic relationships and evolution of the Japanese Carabinae ground beetles based on mitochondrial ND5 gene sequences.

The phylogenetic relationships of the Japanese Carabinae ground beetles were analyzed by comparing 1,069 nucleotide sequences in the mitochondrial gene encoding NADH dehydrogenase subunit 5 (ND5). The ND5 phylogenetic tree revealed that the hind-wingless Carabina and the hind-winged Calosoma/Campalita (Calosomina) diverged from the common ancestor, and Cychrus (Cychrini) is the outgroup of them. Five distinct clusters (groups) can be recognized in the Carabina, i.e., CARABUS, HEMICARABUS, LEPTOCARABUS, APOTOMOPTERUS, and PROCRUSTES/DAMASTER. The ancestors of these lineages diverged almost at the same time more than 10 Myr ago. The Carabus cluster includes two subclusters, Carabus and Ohomopterus. Two species of Carabus examined are phylogenetically rather remote, while five species among Ohomopterus are closely related to each other. The results suggest that diversification of Carabus started much earlier than that of Ohomopterus, presumably in the Eurasian continent, and that of Ohomopterus in the Japanese archipelago. The branching order in the LEPTOCARABUS lineage was established, Authenocarabus/Pentacarabus being their outgroup. In the DAMASTER/PROCRUSTES lineage, Procrustes is placed as the outgroup of Damaster, with the branching order of Coptolabrus and Acoptolabrus/Damaster. The diversification of the Damaster subspecies appeared to have occurred in the Japanese archipelago earlier than Ohomopterus, and its phylogeny reflects their geographic distribution in the archipelago rather than the morphological characters.

Animals↗
PubMed2004

Monophyly of beta-tubulin and H+-ATPase gene variants in Glomus intraradices: consequences for molecular evolutionary studies of AM fungal genes.

Arbuscular mycorrhizal fungi (AMF) are an ecologically important group of fungi. Previous studies showed the presence of divergent copies of beta-tubulin and V-type vacuolar H+-ATPase genes in AMF genomes and suggested horizontal gene transfer from host plants or mycoparasites to AMF. We sequenced these genes from DNA isolated from an in vitro cultured isolate of Glomus intraradices that was free of any obvious contaminants. We found two highly variable beta-tubulin sequences and variable H+-ATPase sequences. Despite this high variation, comparison of the sequences with those in gene banks supported a glomeromycotan origin of G. intraradices beta-tubulin and H+-ATPase sequences. Thus, our results are in sharp contrast with the previously reported polyphyletic origin of those genes. We present evidence that some highly divergent sequences of beta-tubulin and H+-ATPase deposited in the databases are likely to be contaminants. We therefore reject the prediction of horizontal transfer to AMF genomes. High differences in GC content between glomeromycotan sequences and sequences grouping in other lineages are shown and we suggest they can be used as an indicator to detect such contaminants. H+-ATPase phylogeny gave unexpected results and failed to resolve fungi as a natural group. beta-Tubulin phylogeny supported Glomeromeromycota as sister group of the Chytridiomycota. Contrasts between our results and trees previously generated using rDNA sequences are discussed.

Base Composition↗
PubMed2004

Recurrent ecological adaptations revealed through a molecular analysis of the secretive cophyline frogs of Madagascar.

The cophyline microhylid frogs of Madagascar show a wide range of habitat specialization, ranging from terrestrial/burrowing and semi-arboreal to entirely arboreal species. The classification of these frogs is thus far mainly based upon morphological, largely osteological, characters that might be homoplastic. Using 1173 bp of DNA sequences from the mitochondrial 12S and 16S rRNA genes, we here present a molecular phylogeny for 28 species of all known genera, except for the genus Madecassophryne. The resulting maximum likelihood tree contained four major clades: one represented by the genus Anodonthyla, the second by Cophyla and Platypelis, the third by several terrestrial and semi-arboreal species of the genus Plethodontohyla, and the fourth by species of the genera Stumpffia, Plethodontohyla, and Rhombophryne. The results confirm that several cophyline lineages adapted independently to similar habitats, with multiple shifts among terrestriality and arboreality. The direction of these shifts cannot be ascertained due to unclarified relationships among the most basal lineages, but for one terrestrial species (Anodonthyla montana), it is most parsimonious to assume that it evolved from arboreal ancestors. Our results suggest that the genus Plethodontohyla is probably paraphyletic, and that the classification of this and of the genus Rhombophryne needs to be re-assessed.

Adaptation, Physiological↗
PubMed2006

A molecular phylogeny of New Zealand's Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences.

The New Zealand robin (Petroica australis), tomtit (P. macrocephala), and Chatham Island black robin (P. traversi) are members of the Petroicidae family of Australo-Papuan robins, found throughout Australasia and the western Pacific. In the nearly 200 years since the New Zealand members of Petroicidae were first described, the division of species, subspecies, and even genera has undergone many changes. In this study, we investigate whether molecular phylogenies based on mitochondrial DNA sequences support current taxonomic classifications based on morphology. Petroica traversi, P. australis, and P. macrocephala form distinct clades in phylogenetic trees constructed from Cytochrome b and control region sequences, however the position of the black robin is at odds with the morphological and behavioral data. The black robin does not appear to be a derivative of the New Zealand robin, instead it groups strongly with the tomtit, indicating that lineage sorting and/or introgressive hybridization may have occurred. There is some evidence to support the hypothesis that two invasions of Petroica from Australia have occurred, however additional data from Australian Petroica taxa are required to confirm this. Control region sequences confirm a deep split between the North and South Island P. australis lineages, but suggest a recent radiation of P. macrocephala.

Animals↗
PubMed2026

Nuclear single-copy orthologous genes as phylogenomic markers for resolving the closely related firefly genera Pteroptyx, Medeopteryx, and Trisinuata (Coleoptera: Lampyridae: Luciolinae).

Fireflies (Lampyridae) are bioluminescent beetles with broad ecological roles across temperate and tropical ecosystems, occupying diverse habitats including forests, wetlands, grasslands, mangroves, and riverine systems. The subfamily Luciolinae is primarily distributed across Asia and the Indo-Pacific. Phylogenetic relationships among three closely related Luciolinae genera - Medeopteryx, Pteroptyx, and Trisinuata - remain unresolved using mitochondrial genome data alone. This study used nuclear genome data to resolve relationships among these genera and identify a lighter-weight nuclear marker panel for expanding taxon sampling. Draft genomes were reconstructed for fifteen firefly species, eight from the focal genera, and analyzed with five published firefly genomes. Using BUSCO and OrthoFinder, 1,011 nuclear single-copy orthologs (SCOs) were identified for phylogenomic inference. Discordance between concatenation- and coalescence-based phylogenies indicated incomplete lineage sorting (ILS). The coalescence-based phylogeny recoveredPteroptyxas monophyletic and sister to a (Medeopteryx,Trisinuata) clade, with Trisinuata nested within a non-monophyletic Medeopteryx; however, quartet support at the base of Pteroptyx, particularly at Pt. valida, was low.Filtering for compositional homogeneity, clock-likeness, and species-tree concordance yielded 103 SCOs with a significantly higher proportion of parsimony-informative sites than non-selected loci, retaining the backbone topology with higher gene concordance support at scored clades, while ILS-driven discordance at Pt. valida persists - confirming that the reduced panel retains phylogenetic resolving power for future taxon sampling. These findings demonstrate a practical framework for using nuclear SCOs to resolve close phylogenetic relationships within Luciolinae. Future work should expand taxon sampling - especially forTrisinuata - alongside long-read assemblies, for a more robust phylogenomic framework.

Fireflies↗
PubMed2003

Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".

The basal actinopterygians comprise four major lineages (polypteriforms, acipenseriforms, lepisosteids, and Amia) and have been collectively called "ancient fish." We investigated the phylogeny of this group of fishes in relation to teleosts using mitochondrial genomic (mitogenomic) data, and compared this to the various alternative phylogenetic hypotheses that have been proposed previously. In addition to the previously determined complete mitochondrial DNA (mtDNA) sequences from 14 teleosts and two outgroups, we used newly determined mitogenomic sequences of 12 purposefully chosen species representing all the ancient fish lineages plus related teleosts. This data set comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and third codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) and these data were subjected to maximum parsimony, maximum likelihood, and Bayesian analyses. The resultant trees from the three methods were well resolved and largely congruent, with most internal branches being supported by high statistical values. Mitogenomic data strongly supported not only the monophyly of the teleosts (osteoglossomorphs and above), but also a sister-group relationship between the teleosts and a clade comprising the acipenseriforms, lepisosteids, and Amia, with the polypteriforms occupying the most basal position in the actinopterygian phylogeny. Although the tree topology differed from any of the previously proposed hypotheses based on morphology, it exhibited congruence with a recently proposed novel hypothesis based on nuclear markers.

Animals↗
PubMed2006

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain.

The division of the living world into three cellular domains, Archaea, Bacteria, and Eukarya, is now generally accepted. However, there is no consensus about the evolutionary relationships among these domains, because all of the proposed models have a number of more or less severe pitfalls. Another drawback of current models for the universal tree of life is the exclusion of viruses, otherwise a major component of the biosphere. Recently, it was suggested that the transition from RNA to DNA genomes occurred in the viral world, and that cellular DNA and its replication machineries originated via transfers from DNA viruses to RNA cells. Here, I explore the possibility that three such independent transfers were at the origin of Archaea, Bacteria, and Eukarya, respectively. The reduction of evolutionary rates following the transition from RNA to DNA genomes would have stabilized the three canonical versions of proteins involved in translation, whereas the existence of three different founder DNA viruses explains why each domain has its specific DNA replication apparatus. In that model, plasmids can be viewed as transitional forms between DNA viruses and cellular chromosomes, and the formation of different levels of cellular organization (prokaryote or eukaryote) could be traced back to the nature of the founder DNA viruses and RNA cells.

Archaea↗
PubMed2004

Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants.

Some group II introns in the organelle genomes of plants and algae are disrupted and require trans-splicing of the affected exons from independent transcripts. A peculiar mitochondrial nad5 gene structure is universally conserved in flowering plants where two trans-splicing introns frame a tiny exon of only 22 nucleotides, and two additional conventional group II introns interrupt the nad5 reading frame at other sites. These four introns are absent in the liverwort Marchantia polymorpha, which carries a group I intron at an unrelated site in nad5. To determine how intron gains and losses have sculptured mitochondrial gene structures in early land-plant evolution, we have investigated the full nad5 gene structures in the three bryophyte classes and the fern Asplenium nidus. We find the single Marchantia group I intron nad5i753 present as the only intervening sequence in both closely (Corsinia and Monoclea) and distantly related (Noteroclada, Bazzania, and Haplomitrium) liverwort genera. In a taxonomically wide spectrum of mosses (Sphagnum, Encalypta, Timmia, Ulota, and Rhacocarpus); however, we additionally identify the angiosperm-type group II introns nad5i230 and nad5i1455. The latter is a cis-arranged homolog to one of the two angiosperm trans-splicing introns, notably the first of its kind in mosses. In the hornwort Anthoceros, the "moss and liverwort-type" group I intron nad5i753 is absent, and, besides nad5i230 and nad5i1455, intron nad5i1477 is present as the second ancestral group II intron which has evolved into a trans-splicing arrangement in angiosperms. The influence of highly frequent RNA editing, most notably in the genera Haplomitrium, Anthoceros, and Asplenium, on phylogenetic tree construction is investigated and discussed. Taken together, the data (1) support a sister group relationship of liverworts as a whole to all other embryophytes, (2) indicate loss of a group I and serial entries of group II introns in the nad5 gene during early evolution of the nonliverwort lineage, and (3) propose a placement of hornworts as sister group to tracheophytes.

Amino Acid Sequence↗
PubMed2004

Nonuniform concerted evolution and chloroplast capture: heterogeneity of observed introgression patterns in three molecular data partition phylogenies of Asian Mitella (saxifragaceae).

Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ribosomal external transcribed spacer (ETS) region, and internal transcribed spacer (ITS) regions, we construct three phylogenetic trees of Asian species of Mitella (Saxifragaceae), a genus of perennials in which natural hybrids are commonly observed. Within this genus, there is a significant topological conflict between chloroplast and nuclear phylogenies and also between the ETS and the ITS, which can be attributed to frequent hybridization within the lineage. Chloroplast DNAs show the most extensive introgression pattern, ITS regions show a moderate pattern, and the ETS region shows no evidence of introgression. Nonuniform concerted evolution best explains the difference in the introgression patterns between the ETS region and ITS regions, as the sequence heterogeneity of the ITS region within an individual genome is estimated to be twice that of an ETS in this lineage. Significant gene conversion patterns between two hybridizing taxa were observed in contiguous arrays of cloned ETS-ITS sequences, further confirming that only ITS regions have introgressed bidirectionally. The relatively slow concerted evolution in the ITS regions probably allows the coexistence of multiple alleles within a genome, whereas the strong concerted evolution in the ETS region rapidly eliminates heterogeneous alleles derived from other species, resulting in species delimitations highly concordant with those based on morphology. This finding indicates that the use of multiple molecular tools has the potential to reveal detailed organismal evolution processes involving interspecific hybridization, as an individual locus varies greatly in its potential to introgress between species.

Asia↗
PubMed2004

Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae.

Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trnL-F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non-parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break-up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long-distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species-rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.

Annonaceae↗
PubMed2000

A deeply branched novel phylotype found in Japanese paddy soils.

Novel 16S rDNA clones which possibly constitute a sister clade from the two known archaeal lineages, Crenarchaeota and Euryarchaeota, were found in paddy soil environments. Overall signature sequences showed that the clone sequences shared a majority of signature sequence features with the Archaea and Eukarya. However, there were at least nine nucleotides which distinguished the novel clones from the domains Archaea and Eukarya. Phylogenetic trees, drawn by maximum-parsimony, neighbour-joining and maximum-likelihood methods, also supported the unique phylogenetic position of the clones. Both signature sequence and phylogenetic analyses strongly suggest that the novel organisms constitute a new group and their phylogenetic positions are distant from the Crenarchaeota and Euryarchaeota. A specific primer set was designed to detect the presence of the novel group of organisms in terrestrial environments. Specific DNA fragments were amplified from all paddy soil DNAs, suggesting that the novel organisms are widely distributed in rice paddy fields in Japan.

Archaea↗