Basal Branching Pattern Research Articles

18S rDNA sequence-structure phylogeny of the eukaryotes simultaneously inferred from sequences and their individual secondary structures

ObjectiveThe eukaryotic tree of life has been subject of numerous studies ever since the nineteenth century, with more supergroups and their sister relations being decoded in the last years. In this study, we reconstructed the phylogeny of eukaryotes using complete 18S rDNA sequences and their individual secondary structures simultaneously. After the sequence-structure data was encoded, it was automatically aligned and analyzed using sequence-only as well as sequence-structure approaches. We present overall neighbor-joining trees of 211 eukaryotes as well as the respective profile neighbor-joining trees, which helped to resolve the basal branching pattern. A manually chosen subset was further inspected using neighbor-joining, maximum parsimony, and maximum likelihood analyses. Additionally, the 75 and 100 percent consensus structures of the subset were predicted.ResultsAll sequence-structure approaches show improvements compared to the respective sequence-only approaches: the average bootstrap support per node of the sequence-structure profile neighbor-joining analyses with 90.3, was higher than the average bootstrap support of the sequence-only profile neighbor-joining analysis with 73.9. Also, the subset analyses using sequence-structure data were better supported. Furthermore, more subgroups of the supergroups were recovered as monophyletic and sister group relations were much more comparable to results as obtained by multi-marker analyses.

18S rDNA sequence-structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida).

The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence-structure data are encoded and automatically aligned. Here, we present a sequence-structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence-structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.

Molecular phylogeny, biogeography and chromosome evolution of Malagasy dwarf geckos of the genus Lygodactylus (Squamata, Gekkonidae)

We performed a phylogenetic analysis using nuclear (RAG‐1, RAG‐2) and mitochondrial (16S) markers, a statistical Bayesian reconstruction of ancestral distribution areas and a karyological analysis on most Malagasy species of the gekkonid genus Lygodactylus. The phylogenetic analysis largely confirms major basal branching pattern of previous molecular studies, but highlights significant differences concerning both the relationships between different species groups as well as those within groups. The biogeographic analysis supports a Malagasy origin of Lygodactylus, an oversea dispersal to continental Africa and a return to Madagascar. The L. madagascariensis group (also including a new candidate species identified herein) is the most basal clade in Lygodactylus, and the sister group of a clade with all the remaining species. The second most basal clade is the L. verticillatus group, placed as the sister group of a clade comprising African and Malagasy species. The sister lineage of the L. verticillatus group originated the African radiation through an oversea dispersal out of Madagascar. Eventually, the sister lineage of the L. capensis group originated secondary dispersals from Africa to Madagascar. In Madagascar, lineage diversification in different species groups mainly occurred from southern to northern and eastern regions. Dispersal, vicariance and paleoclimatic refugia probably played a relevant role in the evolutionary history of closely related taxa and in speciation mechanisms. The cytogenetic analysis evidenced a high karyotypic variability in Lygodactylus (from 2n = 34 to 2n = 40), which is at least partly consistent with the phylogenetic relationships and the composition of the various species group. Chromosome evolution occurred independently in different lineages, mainly through a reduction in the chromosome number and starting from a putative primitive karyotype of 2n = 40 with all telocentric elements.

Muscle Glycogen Remodeling and Glycogen Phosphate Metabolism following Exhaustive Exercise of Wild Type and Laforin Knockout Mice

Glycogen, the repository of glucose in many cell types, contains small amounts of covalent phosphate, of uncertain function and poorly understood metabolism. Loss-of-function mutations in the laforin gene cause the fatal neurodegenerative disorder, Lafora disease, characterized by increased glycogen phosphorylation and the formation of abnormal deposits of glycogen-like material called Lafora bodies. It is generally accepted that the phosphate is removed by the laforin phosphatase. To study the dynamics of skeletal muscle glycogen phosphorylation in vivo under physiological conditions, mice were subjected to glycogen-depleting exercise and then monitored while they resynthesized glycogen. Depletion of glycogen by exercise was associated with a substantial reduction in total glycogen phosphate and the newly resynthesized glycogen was less branched and less phosphorylated. Branching returned to normal on a time frame of days, whereas phosphorylation remained suppressed over a longer period of time. We observed no change in markers of autophagy. Exercise of 3-month-old laforin knock-out mice caused a similar depletion of glycogen but no loss of glycogen phosphate. Furthermore, remodeling of glycogen to restore the basal branching pattern was delayed in the knock-out animals. From these results, we infer that 1) laforin is responsible for glycogen dephosphorylation during exercise and acts during the cytosolic degradation of glycogen, 2) excess glycogen phosphorylation in the absence of laforin delays the normal remodeling of the branching structure, and 3) the accumulation of glycogen phosphate is a relatively slow process involving multiple cycles of glycogen synthesis-degradation, consistent with the slow onset of the symptoms of Lafora disease.

Phylogeography and Population Genetic Structure of Amur Grayling Thymallus grubii in the Amur Basin.

Amur grayling, Thymallus grubii, is an important economic cold freshwater fish originally found in the Amur basin. Currently, suffering from loss of habitat and shrinking population size, T. grubii is restricted to the mountain river branches of the Amur basin. In order to assess the genetic diversity, population genetic structure and infer the evolutionary history within the species, we analysised the whole mitochondrial DNA control region (CR) of 95 individuals from 10 rivers in China, as well as 12 individuals from Ingoda/Onon and Bureya River throughout its distribution area. A total of 64 variable sites were observed and 45 haplotypes were identified excluding sites with gaps/missing data. Phylogenetic analysis was able to confidently predict two subclade topologies well supported by maximum-parsimony and Bayesian methods. However, basal branching patterns cannot be unambiguously estimated. Haplotypes from the mitochondrial clades displayed local homogeneity, implying a strong population structure within T. grubii. Analysis of molecular variance detected significant differences among the different geographical rivers, suggesting that T. grubii in each river should be managed and conserved separately.

Global Genetic Variation at OAS1 Provides Evidence of Archaic Admixture in Melanesian Populations

Recent analysis of DNA extracted from two Eurasian forms of archaic human shows that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. Although these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We resequenced a 7-kb region encompassing the OAS1 gene in 88 individuals from six Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 myr, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1,500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.

Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon

The avian family Accipitridae has historically been divided into subfamilies or tribes based on features such as general resemblance, feeding ecology, and behavior. Consequently, the monophyly of those groups has been questionable. Recently, three phylogenetic analyses of a majority of the genera have appeared, one based on osteology, one on DNA sequences from a single mitochondrial gene, and the third on mitochondrial plus nuclear DNA sequences, and the resulting phylogenies were in substantial disagreement concerning the composition and basal branching patterns of the clades and hence require further analysis and confirmation. Here we use DNA sequences from the large nuclear RAG-1 exon to investigate the phylogenetic relationships of these birds. Our results largely corroborated the prior study that included nuclear genes. We found strong support for a monophyletic clade comprising the secretarybird Sagittarius serpentarius, the osprey Pandion haliaetus, and the traditional accipitrids. However, every one of the traditionally recognized subfamilies of accipitrids was found to be polyphyletic. The most basal nodes in the phylogeny separate small clades of insectivorous and scavenger species, such as kites and Old World vultures, from the rest of the family. The speciose genera of bird and mammal predators are all relatively derived (terminal) in the phylogeny. Many of the basal clades are cosmopolitan in their distributions, consistent with the great mobility of these raptors. A new classification is proposed that eliminates the problem of polyphyletic intrafamilial taxa.

Endopterygote systematics – where do we stand and what is the goal (Hexapoda, Arthropoda)?

Abstract. Impressive progress has been made recently in the systematics of holometabolous insects. Nevertheless, important questions remain controversial, and uncertainties concerning the relationships of major lineages may even have increased. New analytical techniques have been developed and an immense wealth of molecular data has accumulated. Although no decisive breakthrough has yet been achieved, recent analyses of large molecular datasets have contributed greatly to the reconstruction of the phylogeny of several holometabolous lineages. Extensive combined analyses with substantial morphological datasets and molecular data comprising several genes (‘total evidence’) are still required for a well‐founded phylogenetic hypothesis for the entire group. Endopterygota monophyly is supported mainly by the specific and derived mode of development, which may be considered as a new evolutionary level within Hexapoda. The basal branching pattern remains controversial. A division into two large clades comprising Coleoptera (+ Strepsiptera?) + Neuropterida, on the one hand, and Hymenoptera + [Amphiesmenoptera + Antliophora (including Strepsiptera?)], on the other, appears plausible. Alternative hypotheses have been proposed based on wing characters and molecular data. The position of Strepsiptera remains unsolved. Mecoptera almost certainly is not monophyletic, as Siphonaptera are probably sister to Boreidae. Immense progress has been made in the reconstruction of the intraordinal relationships of all orders, thanks to increasing studies based on combined datasets. Common efforts of morphologists and molecular systematists probably will lead to further rapid progress. Several discoveries of new higher ranking taxa during recent years have revealed that large‐scale habitat destruction will not only have disastrous effects on global biodiversity, but also on the study of insect phylogeny and evolution.

Local Diameter Fully Constrains Dendritic Size in Basal but not Apical Trees of CA1 Pyramidal Neurons

Computational modeling of dendritic morphology is a powerful tool for quantitatively describing complex geometrical relationships, uncovering principles of dendritic development, and synthesizing virtual neurons to systematically investigate cellular biophysics and network dynamics. A feature common to many morphological models is a dependence of the branching probability on local diameter. Previous models of this type have been able to recreate a wide variety of dendritic morphologies. However, these diameter-dependent models have so far failed to properly constrain branching when applied to hippocampal CA1 pyramidal cells, leading to explosive growth. Here we present a simple modification of this basic approach, in which all parameter sampling, not just bifurcation probability, depends on branch diameter. This added constraint prevents explosive growth in both apical and basal trees of simulated CA1 neurons, yielding arborizations with average numbers and patterns of bifurcations extremely close to those observed in real cells. However, simulated apical trees are much more varied in size than the corresponding real dendrites. We show that, in this model, the excessive variability of simulated trees is a direct consequence of the natural variability of diameter changes at and between bifurcations observed in apical, but not basal, dendrites. Conversely, some aspects of branch distribution were better matched by virtual apical trees than by virtual basal trees. Dendritic morphometrics related to spatial position, such as path distance from the soma or branch order, may be necessary to fully constrain CA1 apical tree size and basal branching pattern.

Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)

BackgroundIn phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be unambiguously estimated by the usual methods (maximum parsimony (MP), neighbor-joining (NJ), or maximum likelihood (ML)), nor are they well supported. We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades.ResultsOur estimator of profile distances generalizes the maximum likelihood estimator of sequence distances. The basal branching pattern can be estimated by any distance-based method, such as neighbor-joining. Our method (profile neighbor-joining, PNJ) then inherits the accuracy and robustness of profiles and the time efficiency of neighbor-joining.ConclusionsPhylogenetic analysis of Chlorophyceae with traditional methods (MP, NJ, ML and MrBayes) reveals seven well supported subclades, but the methods disagree on the basal branching pattern. The tree reconstructed by our method is better supported and can be confirmed by known morphological characters. Moreover the accuracy is significantly improved as shown by parametric bootstrap.

Phylogeny and classification of the extant basal lineages of the Hymenoptera (Insecta)

The phylogeny of the basal hymenopteran lineages, including representatives of all ‘symphytan’ families, is anal; In total, 236 morphological characters were scored for 44 exemplars, including six outgroup, two xyelic tenthredinoid, five pamphilioid, three cephoid, five ‘siricoid’, one orussid, and six apocritan taxa. The datas analysed with parsimony under equal weights and under implied weights. The monophyly of the Hymenopte strongly supported but the sistergroup of the Hymenoptera cannot be identified with confidence. The relations of the ‘symphytan’ lineages are Xyeloidea +(Tenthredinoidea+ (Pamphilioidea + (Cephoidea + (Ariaxyelic (Siricidae + (Xiphydriidae +(Orussoidea+Apocrita))))))). Many of the relationships between the superfamilies, especially in the basal branching pattern, are only weakly corroborated. The monophyly of most superfamilies is supported, and all may be monophyletic except the ‘Siricoidea’, which is clearly paraphyletic. It is difficult to di whether the Siricidae or the Anaxyelidae are the closest relatives of Xiphydriidae + (Orussoidea + Apocrita). support for the sistergroup relationship between the Orussoidea and the Apocrita is substantial, putative apomorphies being provided by most character systems. There is also good evidence in favour of the monophj the Apocrita. The internal phylogeny of the Tenthredinoidea differs considerably from the results of earlier anal The Blasticotomidae are the sistergroup of the Tenthredinoidea s.s. Relationships at the base of the Tenthredini s.s. are weakly supported. It is uncertain whether the Tenthredinidae are monophyletic or comprise a 1 paraphyletic grade within the Tenthredinoidea s.s. The Diprionidae may be the sistergroup to Cimbicidae +(Argidae+ Pergidae). Most relationships within the Cimbicidae + (Argidae + Pergidae) clade are corroborated, with the exception of the monophyly of the Argidae. It is proposed to elevate the Anaxyelidae the Xiphydriida both to superfamily status. The family-level classification of the Tenthredinoidea will probably have to be changed, but this must await further clarification of the phylogeny of this superfamily.

Phylogeny and classification of the extant basal lineages of the Hymenoptera (Insecta)

The phylogeny of the basal hymenopteran lineages, including representatives of all «symphytan» families, is analysed. In total, 236 morphological characters were scored for 44 exemplars, including six outgroup, two xyelid, 16 tenthredinoid, five pamphilioid, three cephoid, five «siricoid», one orussid, and six apocritan taxa. The dataset is analysed with parsimony under equal weights and under implied weights. The monophyly of the Hymenoptera is strongly supported but the sistergroup of the Hymenoptera cannot be identified with confidence. The relationships of the «symphytan» lineages are Xyeloidea+(Tenthredinoidea+(Pamphilioidea+(Cephoidea+(Anaxyelidae+ (Siricidae+(Xiphydriidae+(Orussoidea+Apocrita))))))). Many of the relationships between the superfamilies, especially in the basal branching pattern, are only weakly corroborated. The monophyly of most superfamilies is well supported, and all may be monophyletic except the «Siricoidea», which is clearly paraphyletic. It is difficult to decide whether the Siricidae or the Anaxyelidae are the closest relatives of Xiphydriidae+(Orussoidea+Apocrita). The support for the sistergroup relationship between the Orussoidea and the Apocrita is substantial, putative synapomorphies being provided by most character systems. There is also good evidence in favour of the monophyly of the Apocrita. The internal phylogeny of the Tenthredinoidea differs considerably from the results of earlier analyses. The Blasticotomidae are the sistergroup of the Tenthredinoidea s.s. Relationships at the base of the Tenthredinoidea s.s. are weakly supported. It is uncertain whether the Tenthredinidae are monophyletic or comprise a basal paraphyletic grade within the Tenthredinoidea s.s. The Diprionidae may be the sistergroup to the Cimbicidae+(Argidae+Pergidae). Most relationships within the Cimbicidae+(Argidae+Pergidae) clade are well corroborated, with the exception of the monophyly of the Argidae. It is proposed to elevate the Anaxyelidae and the Xiphydriida both to superfamily status. The family-level classification of the Tenthredinoidea will probably also have to be changed, but this must await further clarification of the phylogeny of this superfamily.

Preliminary phylogenetic analysis of selected subterranean amphipod crustaceans, using small subunit rDNA gene sequences

Abstract The exclusively subterranean amphipod genus Bactrurus (Crangonyctidae) occurs in central and eastern parts of the United States. Bactrurus is characterized by morphologically similar species. In at least one instance, the distinction between separate species and geographic variants appears to be blurred. A sequence analysis of the small subunit (18S) rDNA gene was conducted for eight amphipod taxa. Both maximum likelihood and distance methods resulted in phylogenies for several species of Bactrurus that are in accordance with morphological data. These results could not be validated by a parsimony analysis. All three methods of phylogenetic inference, however, produced identical basal branching patterns. The molecular analyses do not support the recognition of what initially appeared to be a new species of Bactrurus from glaciated areas in Montgomery County, Illinois.

Phylogenetic Relationships in Anemone (Ranunculaceae) Based on Morphology and Chloroplast DNA

-Phylogenetic relationships of 36 species of Anemone (Ranunculaceae) and seven related genera were explored with three independent data sets: chloroplast DNA restriction sites, nuclear ribosomal DNA restriction fragments, and morphological/cytological variation. In the chloroplast DNA work, 245 phylogenetically informative restriction sites were identified using ten restriction enzymes. The phylogeny based on conventional data was derived from 27 characters for the same taxa used in the molecular work. A subset of species complexes was examined with additional chloroplast and nuclear ribosomal DNA data. Molecular and morphological characters established Clematis as the most suitable outgroup for the phylogenetic analyses. Many of the terminal groups of the cladograms resulting from the molecular and morphological data sets were similar, but basal branching patterns were substantially different. Because the molecular tree was substantially less homoplastic and had higher bootstrap and decay values than the morphological tree, it was accepted as the more reliable in determining basal relationships. Both morphological and chloroplast DNA phylogenies demonstrate that few of the sections of Anemone as established by previous classifications are monophyletic. The phylogenies based on chloroplast DNA restriction sites and the combined data sets indicate that Pulsatilla, Hepatica, and Knowltonia should be subsumed within Anemone. Various morphological characters indicate that Barneoudia and Oreithales should also be included within the genus Anemone. Independent data sets provide phylogenetic hypotheses useful in interpretations of character evolution. A preliminary, revised classification is proposed. Several hypotheses are offered to explain the unusual geographic distributions found in Anemone. Anemone s. str. consist of 70-90 species of perennial, low-growing herbs (Ulbrich 1905-1906; pers. obs.). The genus is characterized by a rosette of basal leaves, an involucrate peduncle bearing a single flower or compound inflorescence, a perianth of petaloid sepals, and an achene fruit. There is considerable morphological variation within the genus. The perennating structures are upright stems, rhizomes, or tubers. The basal leaves vary from trilobed to several times ternate, rarely pinnate. The involucral leaves are various in number and form, sometimes reduced and bract-like. The achenes are glabrous to tomentose, few to many in number, with various morphologies of the style. Base chromosome numbers are either seven or eight. Species are most numerous in the Northern Hemisphere, but also occur in mountainous and cooler regions of the Southern Hemisphere. They inhabit a wide range of habitats including arctic and alpine tundra, prairie, woodlands, Mediterannean regions, and semidesert. Several previous classifications placed Anemone and Clematis in the same tribe, Anemoneae (Langlet 1932; Tamura 1967). A sister genus to Clematis from Africa, Clematopsis, should also be included in this tribe (Hutchinson 1920). Anemoneae are regarded as most closely related to the tribes Ranunculeae and Adonieae. Cladistic analyses based on morphology of the Ranunculaceae (Hoot 1991) place Anemone in a clade with Clematis, Hepatica, Pulsatilla, and Ranunculus, united by two derived character states, presence of achenes and the chemical compound ranunculin. It is not at all clear which of these genera are most closely related to Anemone. The delimitation of Anemone has been debated for years. Early classifications often included the genera Hepatica, Pulsatilla, Knowltonia, Barneoudia, and Oreithales within Anemone (Jan-