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PubMed2005

Phylogenetic investigation of Dogiel's pericellular nests and Cajal's initial glomeruli in the dorsal root ganglion.

Cajal's initial glomeruli (IG) and Dogiel's pericellular nests (PCNs) were first described from methylene blue preparations of healthy animal tissues around the beginning of the last century. Since that time, although many reports have been published concerning these structures, few have focused on their development and phylogeny in healthy animals. The aim of this study was to examine the phylogenetic development of the sensory neurons in Cajal's IG (also called axonal glomeruli) and Dogiel's PCNs in the dorsal root ganglion (DRG) of the healthy adult frog, chick, rat, and rabbit. The three-dimensional architecture of the neurons was observed in ganglia by scanning electron microscopy after removal of the connective tissue. The neurons in the DRG of fish are known to be bipolar, but DRG neurons in the species examined here were found to be pseudounipolar, with single stem processes. The proportion of neurons having IG or PCNs increased with increasing phylogenetic complexity in the species examined here. Cajal's initial glomeruli, the convolution of the stem process near the parent cell body: In frogs, the ganglia were small and the neuronal stem processes were very short and straight. In chicks, the stem processes were longer; sometimes very long, tortuous processes were observed. However, no neurons with typical IG were observed in either species. Typical IG were observed in rats and rabbits; their occurrence was much more frequent in rabbits. Pseudounipolarization, i.e., the transition from bipolar to pseudounipolar neurons, is thought to save space, limit the length of neuronal processes, and reduce conduction time. However, an explanation of the evolutionary advantage of the IG, which is formed by the excessive prolongation of the stem process, remains elusive. The cytological and electrophysiological importance of IG has been discussed. Dogiel's pericellular nests (PCNs), which resemble balls of yarn made of thin unmyelinated nerve fibers around DRG neurons, have been observed in the DRG of rats and rabbits, but not in frogs or chicks. This interesting structure shows not only ontogenetic development in healthy animals but also phylogenetic development among species. The nerve fibers in the PCNs were less than 1.2 mum in diameter and had some varicosities. An immunohistochemical study using anti-tyrosine hydroxylase (TH) antibody revealed that some PCNs contain TH-positive nerve fibers and varicosities. Such TH-positive PCNs disappear after sympathectomy. These results suggest that the PCNs are made up of autonomic nerve fibers.

Animals↗
PubMed2026

Insights Into the Structural Features, Codon Usage Patterns, and Phylogenetic Analysis in Neoniphon argenteus (Teleostei: Holocentriformes) Based on Complete Mitochondrial Genome.

Neoniphon argenteus, a widely distributed nocturnal coral reef fish in the family Holocentridae, plays an important role in maintaining coral reef ecosystem health, yet its phylogenetic position remains poorly resolved. To bridge this gap, we sequenced and analyzed the complete mitochondrial genome of a specimen from the South China Sea to characterize its structural features, codon usage patterns, and phylogenetic relationships. The 16,569 bp mitogenome (GenBank: PP190474.1) encodes 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions, exhibiting a distinct A + T bias. All tRNAs fold into typical cloverleaf secondary structures except tRNA-Ser (AGN), which lacks the dihydrouridine (DHU) arm. The control region contains palindromic motifs (TACAT/ATGTA) capable of forming hairpin structures and five conserved sequence blocks, whereas the OL region harbors a conserved 5'-GCCGG-3' motif. RSCU analysis revealed 31 frequently used codons (RSCU > 1) with a pronounced preference for A/C-ending codons. The ΔRSCU method identified 10 candidate optimal codons (GCA, CAA, GAA, GGA, AUU, CUA, CCA, CGA, ACA, and GUC). Selection pressure analysis using EasyCodeML and site-specific models indicated that all PCGs are predominantly under purifying selection, with no significant evidence of pervasive positive selection. ND6 exhibited elevated pairwise Ka/Ks ratios (mean = 1.209 ± 0.047), consistent with reduced selective constraint rather than adaptive evolution. Phylogenetic analysis of 19 Holocentriformes species using maximum likelihood and Bayesian inference with partitioned models based on 13 PCGs and two rRNA genes (12S and 16S) assigned all taxa to two well-supported subfamilies (Holocentrinae and Myripristinae). Within Holocentrinae, Neoniphon species form a monophyletic clade nested within a paraphyletic Sargocentron, suggesting that the genus Sargocentron as currently defined is not monophyletic. This study provides useful baseline molecular data for further exploration of the evolutionary history of N. argenteus and other members of Holocentriformes.

Holocentridae↗
PubMed1993

Uses and limitations of mammalian fetal membranes and placenta for phylogenetic reconstruction.

Comparative studies on the development of the mammalian fetal membranes and placenta, and discussions of the possible evolutionary significance of these data, have been carried out for more than a century. Throughout much of this period, however, such data were considered in isolation from cranioskeletal and other biological findings, so that only rarely were placental features incorporated into comparative assessments of mammalian evolution. Evolutionary interpretations of the fetal membrane evidence were commonly based on the concept of overall similarity, and most placentologists were strongly influenced by the widely accepted hypothesis that living "insectivores" were closely related to the ancestral eutherian mammals. Mossman's emphasis on the use of all available developmental data on the fetal membranes and placenta, rather than simply the nature of the definitive placenta, marked a turning point in the history of using such findings for assessing eutherian mammalian evolution. Recent advances in the methodology of phylogenetic inference, with emphasis on evaluating convergence versus homology, and on distinguishing between relatively primitive versus derived homologous similarities shared by two or more taxa, have provided a sound framework for the phylogenetic analysis of fetal membrane data. Character analysis of mammalian fetal membrane traits provides a mechanism for testing phylogenetic hypotheses formulated by cranioskeletal features. It is emphasized in this study that fetal membrane data have their greatest input into assessing mammalian phylogeny when they are evaluated in conjunction with the available cranioskeletal and molecular evidence.

Animals↗
PubMed2006

Distribution and genetic analysis of TTV and TTMV major phylogenetic groups in French blood donors.

TTV and TTMV (recently assigned to the floating genus Anellovirus) infect human populations (including healthy individuals) at high prevalence (>80%). They display notably high levels of genetic diversity, but very little is known regarding the distribution of Anellovirus genetic groups in human populations. We analyzed the distribution of the major genetic groups of TTV and TTMV in healthy voluntary blood donors using group-independent and group-specific PCR amplifications systems, combined with sequence determination and phylogenetic analysis. Analysis of Anellovirus groups revealed a non-random pattern of group distribution with a predominant prevalence of TTV phylogenetic groups 1, 3, and 5, and of TTMV group 1. Multiple co-infections were observed. In addition, TTMV sequences exhibiting a high genetic divergence with reference sequences were identified. This study provided the first picture of the genetic distribution of the major phylogenetic groups of members of the genus Anellovirus in a cohort of French voluntary blood donors. Obtaining such data from a reference population comprising healthy individuals was an essential step that will allow the subsequent comparative analysis of cohorts including patients with well-characterized diseases, in order to identify any possible relationship between Anellovirus infection and human diseases.

Adolescent↗
PubMed2001

Phylogenetic information improves homology detection.

We present a database search method that is based on phylogenetic trees (treesearch). The method is used to search a protein sequence database for homologs to a protein family. In preparation for the search, a phylogenetic tree is constructed from a given multiple alignment of the family. During the search, each database sequence is temporarily inserted into the tree, thus adding a new edge to the tree. Homology between family and sequence is then judged from the length of this edge. In a comparison of our method to profiles (ISREC pfsearch), two implementations of hidden Markov models (HMMER hmmsearch and SAM hmmscore), and to the family pairwise search (FPS) method on 43 families from the SCOP database based on minimum false-positive counts (min-FPCs), we found a considerable gain in sensitivity. In 69% of the test cases, treesearch showed a min-FPC of at most 50, whereas the two second best methods (hmmsearch and FPS) showed this performance only in 53% cases. A similar impression holds for a large range of min-FPC thresholds. The results demonstrate that phylogenetic information can significantly improve the detection of distant homologies and justify our method as a useful alternative to existing methods.

Algorithms↗
PubMed2006

Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships.

Phylogenetic profiles encode patterns of presence or absence of genes across genomes, and these profiles can be used to assign functional relationships to nonhomologous pairs of proteins (Pellegrini et al., Proc Natl Acad Sci USA 1999;96:4284-4288). Although it is well known that many proteins were created from combinations of domains, most of the existing implementations of phylogenetic profiles do not consider this fact. Here, we introduce an extension that considers the multidomain nature of proteins and test the method against the known interaction data sets. Whereas earlier implementations associated one entire sequence with one protein phylogenetic profile (Single-Profile), our method instead breaks the sequence into a set of segments of predetermined size and constructs a separate profile for each segment (Multiple-Profile). The results show that the Multiple-Profile method performs as well as the Single-Profile method. However, the two methods share, surprisingly, a small fraction of their predictions, indicating that the Multiple-Profile method can detect known interactions missed by the Single-Profile method. Thus, the Multiple-Profile method can be used with other methods to determine functional relationships on a genome scale with wider coverage.

Binding Sites↗
PubMed2000

The evolution of postcopulatory displays in dabbling ducks (Anatini): a phylogenetic perspective.

Although postcopulatory displays are widespread in animals, little is known about their function or the intended receiver. The postcopulatory displays of dabbling ducks are among the best described for any animal group. We documented the presence of initial and additional postcopulatory displays in nearly all dabbling duck species. We then reconstructed the evolution of postcopulatory displays in dabbling ducks using a phylogeny derived from mitochondrial DNA sequences. The display immediately following copulation (the initial display) is highly stereotyped in most species and shows extreme phylogenetic conservation. In contrast, the performance of additional displays is less stereotyped and less phylogenetically conservative. We review the possible functions of postcopulatory displays. Using evidence from display orientation, display form and phylogenetic reconstruction, we suggest that the most likely functions of postcopulatory displays in dabbling ducks are pair bond maintenance, individual identification, or signalling a successful copulation. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed2001

Response to interspecific vocalizations is affected by degree of phylogenetic relatedness in Streptopelia doves.

Owing to common descent, related species often show similarity in a number of traits, including those involved in communication. As a result signal similarity and phylogenetic distance are usually inversly related. However, similarity in signal structure need not correspond with similarity in response to such signals. We tested the hypothesis that individuals are more responsive to signals from closely related species than from distantly related ones. We conducted playback experiments on two turtle dove species (African collared-dove, Streptopelia roseogrisea, and vinaceous dove, Streptopelia vinacea) using conspecific and heterospecific vocalizations. Vocalizations were played from species that differed in degree of relatedness and in relative geographical distribution. This enabled us to separate the effects of phylogeny and those of sympatry. There was an effect of phylogenetic distance, with a decrease in response to playback stimuli as phylogenetic distance increased. The results also suggest a minor effect of sympatry, with the response to sympatric species being lower. Copyright 2001 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed2000

The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae.

Aspergillus flavus is a common filamentous fungus that produces aflatoxins and presents a major threat to agriculture and human health. Previous phylogenetic studies of A. flavus have shown that it consists of two subgroups, called groups I and II, and morphological studies indicated that it consists of two morphological groups based on sclerotium size, called "S" and "L." The industrially important non-aflatoxin-producing fungus A. oryzae is nested within group I. Three different gene regions, including part of a gene involved in aflatoxin biosynthesis (omt12), were sequenced in 33 S and L strains of A. flavus collected from various regions around the world, along with three isolates of A. oryzae and two isolates of A. parasiticus that were used as outgroups. The production of B and G aflatoxins and cyclopiazonic acid was analyzed in the A. flavus isolates, and each isolate was identified as "S" or "L" based on sclerotium size. Phylogenetic analysis of all three genes confirmed the inference that group I and group II represent a deep divergence within A. flavus. Most group I strains produced B aflatoxins to some degree, and none produced G aflatoxins. Four of six group II strains produced both B and G aflatoxins. All group II isolates were of the "S" sclerotium phenotype, whereas group I strains consisted of both "S" and "L" isolates. Based on the omt12 gene region, phylogenetic structure in sclerotium phenotype and aflatoxin production was evident within group I. Some non-aflatoxin-producing isolates of group I had an omt12 allele that was identical to that found in isolates of A. oryzae.

Aflatoxins↗
PubMed2000

Phylogenetic species recognition and species concepts in fungi.

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.

Evolution, Molecular↗
PubMed2001

Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora.

The genera Neurospora and Gelasinospora are conventionally distinguished by differences in ascospore ornamentation, with elevated longitudinal ridges (ribs) separated by depressed grooves (veins) in Neurospora and spherical or oval indentations (pits) in Gelasinospora. The phylogenetic relationships of representatives of 12 Neurospora and 4 Gelasinospora species were assessed with the DNA sequences of four nuclear genes. Within the genus Neurospora, the 5 outbreeding conidiating species form a monophyletic group with N. discreta as the most divergent, and 4 of the homothallic species form a monophyletic group. In combined analysis, each of the conventionally defined Gelasinospora species was more closely related to a Neurospora species than to another Gelasinospora species. Evidently, the Neurospora and Gelasinospora species included in this study do not represent two clearly resolved monophyletic sister genera, but instead represent a polyphyletic group of taxa with close phylogenetic relationships and significant morphological similarities. Ascospore morphology, the character that the distinction between the genera Neurospora and Gelasinospora is based upon,was not an accurate predictor of phylogenetic relationships.

Cloning, Molecular↗
PubMed1999

Ontogenetic and phylogenetic development of the endocrine pancreas (islet organ) in fish.

The morphology of the gastroenteropancreatic (GEP) system of fish was reviewed with the objective of providing the phylogenetic and ontogenetic development of the system in this vertebrate group, which includes agnathans and gnathostome cartilaginous, actinoptyerygian, and sarcopterygian fish. Particular emphasis is placed on the fish homolog of the endocrine pancreas of other vertebrates, which is referred to as the islet organ. The one-hormone islet organ (B cells) of larval lampreys is the most basic pattern seen among a free-living vertebrate, with the two-hormone islet organ (B and D cells) of hagfish and the three-hormone islet organ (B, D, and F cells) of adult lampreys implying a phylogenetic trend toward the classic four-hormone islet tissue (B, D, F, and A cells) in most other fish. An earlier stage in the development of this phylogenetic sequence in vertebrates may have been the restriction of islet-type hormones to the alimentary canal, like that seen in protochordates. The relationship of the islet organ to exocrine pancreatic tissue, or its equivalent, is variable among bony, cartilaginous, and agnathan fishes and is likely a manifestation of the early divergence of these piscine groups. Variations in pancreatic morphology between individuals of subgroups within both the lamprey and chondrichthyan taxa are consistent with their evolutionary distance. A comparison of the distribution and degree of concentration of the components of the islet organ among teleosts indicates a diffuse distribution of relatively small islets in the generalized euteleosts and the tendency for the concentration into Brockmann bodies of large (principal) islets (with or without secondary islets) in the more derived forms. The holostean actinopterygians (Amiiformes and Semiontiformes) share with the basal teleosts (osteoglossomorphs, elopomorphs) the diffuse arrangement of the components of the islet organ that is seen in generalized euteleosts. Since principal islets are also present in adult lampreys the question arises whether principal islets are a derived or a generalized feature among teleosts. There is a paucity of studies on the ontogeny of the GEP system in fish but it has been noted that the timing of the appearance of the islet cell types parallels the time that they appear during phylogeny; the theory of recapitulation has been revisited. It is stressed that the lamprey life cycle provides a good opportunity for studying the development of the GEP system. There are now several markers of cell differentiation in the mammalian endocrine pancreas which would be useful for investigating the development of the islet organ and cells of the remaining GEP system in fish.

Animals↗
PubMed2000

Islet hormones from the African bullfrog Pyxicephalus adspersus (Anura:Ranidae): structural characterization and phylogenetic implications.

The African bullfrog Pyxicephalus adspersus is generally classified along with frogs of the genus Rana in the subfamily Raninae of the family Ranidae but precise phylogenetic relationships between species are unclear. Pancreatic polypeptide (PP), insulin, and glucagon-like peptide (GLP-1) were isolated from an extract of P. adspersus pancreas and characterized structurally. A comparison of the amino acid sequence of Pyxicephalus PP (APSEPQHPGG(10)QATPEQLAQY(20)YSDLYQYITF(30)ITRPRF++ +. NH(2)) with those of the known amphibian PP molecules in a maximum parsimony analysis generates a single phylogenetic tree in which Pyxicephalus is the sister to the clade comprising the members of the genus Rana. The three orders of living amphibians form discrete clades with the representative of the Gymnophiona appearing as sister to the Caudata-Anura. In contrast, Pyxicephalus insulin (A chain, GIVEQCCHSA(10)CSLYDLENYC(20)N; B-chain, LANQHLCGSH(10)LVEALYMVCG(20)ERGFFYYPKS(30)) and and GLP-1 (HAEGTFTSDM(10)TSYLEEKAAK(20)EFVDWLIKGR(30)PK) resemble more closely the corresponding peptides from the cane toad Bufo marinus than the peptides from any species of Rana. Cladistic analysis based upon the amino acid sequences of insulin produced a polyphyletic assemblage with the Gymnophiona nesting within an unresolved clade containing the non-ranid frogs. The data support the assertion that the amino acid sequence of PP, but not those of the other islet hormones, is of value as a molecular marker for inferring phylogenetic relationships between early tetrapod species.

Amino Acid Sequence↗
PubMed2000

The phylogenetic affinities of Otavipithecus namibiensis.

The middle Miocene hominoid Otavipithecus namibiensis is the first and most complete fossil ape from sub-equatorial Africa and represents a significant addition to the taxonomically sparse African middle Miocene hominoid fossil record. The Otavipithecus hypodigm comprises the holotype mandible, which presents a unique mosaic of dental and gnathic characters, and several attributed cranial and postcranial elements which resemble the stem hominoid Proconsul. Contrary to initial hopes that this discovery would provide new insights into hominoid morphological diversity and phylogenetic relationships, a variety of conflicting phylogenetic hypotheses have been advanced suggesting ties to virtually every major large-bodied hominoid group (Conroy et al., 1992; Andrews, 1992 a; Conroy, 1994; Pickford et al., 1994; Begun, 1994 a). Cladistic analysis of a matrix of 22 qualitative and ten quantitative characters of the mandible and mandibular dentition found no support for a close phylogenetic relationship between Otavipithecus and either the African ape or great ape clades, or with any of the Eurasian fossil hominoids with which it has previously been compared. A close relationship between Otavipithecus and Kenyapithecus cannot be ruled out, but is deemed unlikely on the basis both of morphological comparisons and the absence of support within a cladistic framework. The present analysis indicates that Otavipithecus is most closely related to Afropithecus, as previously suggested by Andrews (1992 a) among others. Due to lack of statistical support for this result, a conservative interpretation, that these taxa represented related but divergent lineages of a late early Miocene hominoid radiation, is currently favored. Findings are consistent with the allocation of Otavipithecus to Andrews' (1992 a) tribe Afropithecini which represents the sister group to Kenyapithecus and the extant ape clade.

Africa↗
PubMed2001

Human genetic disorders, a phylogenetic perspective.

When viewed from the perspective of time, human genetic disorders give new insights into their etiology and evolution. Here, we have correlated a specific set of Alu repetitive DNA elements, known to be the basis of certain genetic defects, with their phylogenetic roots in primate evolution. From a differential distribution of Alu repeats among primate species, we identify the phylogenetic roots of three human genetic diseases involving the LPL, ApoB, and HPRT genes. The different phylogenetic age of these genetic disorders could explain the different susceptibility of various primate species to genetic diseases. Our results show that LPL deficiency is the oldest and should affect humans, apes, and monkeys. ApoB deficiency should affect humans and great apes, while a disorder in the HPRT gene (leading to the Lesch-Nyhan syndrome) is unique to human, chimpanzee, and gorilla. Similar results can be obtained for cancer. We submit that de novo transpositions of Alu elements, and saltatory appearances of Alu-mediated genetic disorders, represent singularities, places where behavior changes suddenly. Alus' propensity to spread, not only increased the regulatory and developmental complexity of the primate genome, it also increased its instability and susceptibility to genetic defects and cancer. The dynamic spread not only provided markers of primate phylogeny, it must have actively shaped the course of that phylogeny.

Alu Elements↗
PubMed2000

Autoregressive models for estimating phylogenetic and environmental effects: accounting for within-species variations.

Comparative methods are used to investigate the attributes of present species or higher taxa. Difficulties arise from the phylogenetic heritage: taxa are not independent and neglecting phylogenetic inertia can lead to inaccurate results. Within-species variations in life-history traits are also not negligible, but most comparative methods are not designed to take them into account. Taxa are generally described by a single value for each trait. We have developed a new model which permits the incorporation of both the phylogenetic relationships among populations and within-species variations. This is an extension of classical autoregressive models. This family of models was used to study the effect of fishing on six demographic traits measured on 77 populations of teleost fishes.

Animals↗
PubMed1994

Phylogenetic analysis of green plant rbcL sequences.

DNA and derived amino acid sequences of the rbcL gene from selected photosynthetic bacteria, green algae, bryophytes, "fern allies," ferns, and seed plants were used to construct phylogenetic trees using parsimony algorithms. Internal support of clades was determined by the bootstrap and decay indices. External support was judged by comparison of trees with previous morphological and molecular cladograms. Some clades on all the trees are supported both internally and externally, but all of the trees are characterized by unsupported relationships of the bryophytes and fern allies. Trees produced by analyses of all three DNA positions have the highest levels of internal support, but many clades are still not supported externally or internally. Analyses using only the first and second positions of the DNA sequences and derived amino acid sequences produced trees with odd groupings and low levels of internal support for most of the clades. These results indicate that rbcL sequences may be too divergent to test phylogenetic relationships among major groups of green plants. Additional problems with constructing phylogenetic trees from rbcL sequences may be caused by RNA editing, pseudogenes, unequal rates of evolution, and inadequate taxon sampling. Whether RNA editing is a problem can be determined by sequencing amplified RNAs from selected taxa. If pseudogenes are suspected, purified chloroplast DNA should be used for amplification. It may be beneficial to include more taxa in subsequent analyses, but there are indications that historical extinctions will prevent adequate sampling of some groups, such as the bryophytes and fern allies.

Amino Acid Sequence↗
PubMed1994

Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences.

Partial sequences of 28S-like rDNA were amplified using PCR and sequenced for eight species of oyster and one species of mussel. Phylogenetic relationships among seven species of Crassostreinid oyster were inferred from aligned sequences by parsimony and maximum-likelihood methods. Of the 315 sites that varied, 90 were phylogenetically informative in parsimony analysis. Inference by maximum parsimony (MP) is consistent with maximum-likelihood (ML) analysis for the major lineages, yielding a tree with the topology (Mytilus edulis (Ostrea edulis ((Crassostrea rivularis (C. belcheri, C. gigas))(C. virginica, C. rhizophorae, Saccostrea cuccullata, S. commercialis)))). MP and ML analyses resolved the systematic relationships of the Saccostrea and Atlantic Crassostrea differently such that a polytomy linking these four taxa is preferred with the data available. Molecular data support a later divergence of the tropical Pacific Saccostrea from a common ancestor of the Atlantic Crassostrea species. Molecular data from domains D1, D2, and partial D3 of the 28S rDNA supply sufficient phylogenetic information to determine systematic relationships among the extant oyster taxa, from the major species groups to the family level, thus providing valuable characters that are able to supplement the paucity of morphological characters so far recognized.

Animals↗