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Maximum Likelihood Analysis (maximum + likelihood_analysis)
Selected AbstractsParallel evolution of larval morphology and habitat in the snail-killing fly genus TetanoceraJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2006E. G. CHAPMAN Abstract In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat,morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera. [source] Phylogeography and speciation of colour morphs in the colonial ascidian Pseudodistoma crucigasterMOLECULAR ECOLOGY, Issue 10 2004I. TARJUELO Abstract Variation in pigmentation is common in marine invertebrates, although few studies have shown the existence of genetic differentiation of chromatic forms in these organisms. We studied the genetic structure of a colonial ascidian with populations of different colour morphs in the northwestern Mediterranean. A fragment of the c oxidase subunit 1 (COI) mitochondrial gene was sequenced in seven populations of Pseudodistoma crucigaster belonging to three different colour morphs (orange, yellow and grey). Maximum likelihood analyses showed two well-supported clades separating the orange morph from the yellow-grey morphotypes. Genetic divergence between these clades was 2.12%, and ,ST values between populations of the two clades were high (average 0.936), pointing to genetic isolation. Nested clade and coalescence analyses suggest that a past fragmentation event may explain the phylogeographical origin of these two clades. Non-neutral mtDNA evolution is observed in our data when comparing the two clades, showing a significant excess of nonsynonymous polymorphism within the yellow,grey morphotype using the McDonald,Kreitman test, which is interpreted as further support of reproductive isolation. We conclude that the two clades might represent separate species. We compare the population genetic differentiation found with that estimated for other colonial and solitary ascidian species, and relate it to larval dispersal capabilities and other life-history traits. [source] Their Day in the Sun: molecular phylogenetics and origin of photosymbiosis in the ,other' group of photosymbiotic marine bivalves (Cardiidae: Fraginae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009LISA KIRKENDALE The subfamily Fraginae (Cardiidae) is a morphologically diverse group of small-bodied marine clams inhabiting shallow seas worldwide. Like the exclusively photosymbiotic giant clams (Cardiidae: Tridacninae), some fragines are known to host zooxanthellae photosymbionts. However, surveys to widely determine photosymbiotic status and the lack of a comprehensive phylogeny have hindered attempts to track the evolution of photosymbiosis in the group. Worldwide sampling of all fragine genera and subgenera with phylogenetic reconstructions based on four gene regions [nuclear (28S) and mtDNA (16S, cytochrome oxidase I, cytochrome b)] does not support a monophyletic Fraginae. Sampled taxa form four restructured clades: (1) the ,Fragum' group, (2) the ,Trigoniocardia' and ,Ctenocardia' groups, (3) the ,Parvicardium' group and (4) the ,Papillicardium' group. Maximum likelihood analyses strongly support a clade of European cardiids uniting species from three subfamilies. Live examination of > 50% of species reveals that less than half of derived genera and subgenera host photosymbionts, supporting a single and relatively late origin of photosymbiosis in the Fraginae. The evolutionary implications for a small and little modified earliest diverging photosymbiotic lineage are discussed. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 448,465. [source] Direct parametric inference for the cumulative incidence functionJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 2 2006Jong-Hyeon Jeong Summary., In survival data that are collected from phase III clinical trials on breast cancer, a patient may experience more than one event, including recurrence of the original cancer, new primary cancer and death. Radiation oncologists are often interested in comparing patterns of local or regional recurrences alone as first events to identify a subgroup of patients who need to be treated by radiation therapy after surgery. The cumulative incidence function provides estimates of the cumulative probability of locoregional recurrences in the presence of other competing events. A simple version of the Gompertz distribution is proposed to parameterize the cumulative incidence function directly. The model interpretation for the cumulative incidence function is more natural than it is with the usual cause-specific hazard parameterization. Maximum likelihood analysis is used to estimate simultaneously parametric models for cumulative incidence functions of all causes. The parametric cumulative incidence approach is applied to a data set from the National Surgical Adjuvant Breast and Bowel Project and compared with analyses that are based on parametric cause-specific hazard models and nonparametric cumulative incidence estimation. [source] Significance testing of synergistic/antagonistic, dose level-dependent, or dose ratio-dependent effects in mixture dose-response analysisENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 10 2005Martijs J. Jonker Abstract In ecotoxicology, the state of the art for effect assessment of chemical mixtures is through multiple dose,response analysis of single compounds and their combinations. Investigating whether such data deviate from the reference models of concentration addition and/or independent action to identify overall synergism or antagonism is becoming routine. However, recent data show that more complex deviation patterns, such as dose ratio,dependent deviation and dose level,dependent deviation, need to be addressed. For concentration addition, methods to detect such deviation patterns exist, but they are stand-alone methods developed separately in literature, and conclusions derived from these analyses are therefore difficult to compare. For independent action, hardly any methods to detect such deviations from this reference model exist. This paper describes how these well-established mixture toxicity principles have been incorporated in a coherent data analysis procedure enabling detection and quantification of dose level,and dose ratio,specific synergism or antagonism from both the concentration addition and the independent action models. Significance testing of which deviation pattern describes the data best is carried out through maximum likelihood analysis. This analysis procedure is demonstrated through various data sets, and its applicability and limitations in mixture research are discussed. [source] Determination of the inheritance pattern of hyperthelia in cattle by maximum likelihood analysis 1JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2000M. Brka Summary A previously published data-set with observations on supernumerary teats (hyperthelia) in dual-purpose Simmental was reanalysed by maximum-likelihood. The data comprised 537 unrelated animals and 614 members of 27 paternal half-sib families with known phenotype of each sire. The frequency of hyperthelia was 58% in unrelated animals, 51% in families with unaffected sire, and 73% in families with affected sires. Six different cases of single-gene inheritance were considered. The highest log-likelihood was obtained for additive inheritance and for a recessive pattern with 100% penetrance for recessive homozygotes and 32% for both other genotypes. Estimates for the gene frequency of the favourable allele were 0.34 and 0.29, respectively. Simple dominance or recessiveness with full or incomplete penetrance could be excluded. The possibility of finding paternal half-sib families with a heterozygous sire as a resource for a mapping experiment seem to be good in German Simmental. Zusammenfassung Untersuchung des Erbganges für Hyperthelie beim Rind mittels Maximum-Likelihood-Analyse Schon früher veröffentliche Daten mit Beobachtungen zum Auftreten überzähliger Zitzen (Hyperthelie) bei Fleckviehtieren wurden einer Maximum-Likelihood-Analyse unterzogen. Das Material bestand aus 537 unverwandten Tieren und 614 Tieren, die aus 27 verschiedenen väterlichen Halbgeschwistergruppen stammten, wobei der Phänotyp des Vaters jeweils bekannt war. Die relative Häufigkeit überzähliger Zitzen betrug 58% bei unverwandten Tieren, 51% bei Nachkommen von nicht betroffenen Vätern und 73% bei Nachkommen von Vätern, die selbst überzählige Zitzen aufwiesen. Sechs verschiedene Möglichkeiten monogener Vererbung wurden untersucht. Die höchsten Werte für die log-likelihood ergaben sich für einen additiven Erbgang sowie für eine Variante mit 100% Penetranz für die rezessiv Homozygoten und jeweils 32% Penetranz für die beiden anderen Genotypen. Für das erwünschte Allel wurde in beiden Varianten eine ähnliche Frequenz von 34% bzw. 29% geschätzt. Einfache dominante oder rezessive Erbgänge, auch mit unvollständiger Penetranz, konnten ausgeschlossen werden. Die Aussicht, für Kartierungsexperimente geeignete väterlichen Halbgeschwisterfamilien zu finden, scheint für die Rasse Fleckvieh günstig zu sein. [source] Cryptic differentiation and geographic variation in genetic diversity of Hall's Babbler Pomatostomus halliJOURNAL OF AVIAN BIOLOGY, Issue 2 2001Grant I. Miura Sequence variation was examined in domain I of the mitochondrial control region in three Queensland populations of Hall's Babbler Pomatostomus halli, a geographically restricted, monotypic songbird in eastern Australia. Surprisingly, we found that domain I sequences were strongly differentiated into two major clades differing by 3.29%. These two clades exhibited nearly complete geographic concordance with northern and southern populations, except for two haplotypes which were sampled in the north of the range but were phylogenetically allied to the southern clade. We also found a seven-fold higher level of genetic diversity in the northern than in the southern populations. Neutrality and molecular clock tests suggested that selection or differences in substitution rates were not responsible for this difference in diversity. However, a maximum likelihood analysis of gene flow between the north and south suggested that the difference in diversity could be due to both greater population size in the north and asymmetric gene flow dominated by south to north dispersal events. A likelihood ratio test rejected a model in which population sizes were equal and rates of gene flow symmetric, and came close to rejecting a model in which only population sizes were constrained to be equal. These results suggest that different population sizes and asymmetric gene flow could be a major source of differences in genetic variation between populations of Hall's Babbler, although ecological and biogeographic causes for these differences are obscure. [source] A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitatsJOURNAL OF BIOGEOGRAPHY, Issue 4 2010Sergei V. Drovetski Abstract Aim, Boreal forest bird species appear to be divided into lineages endemic to each northern continent, in contrast to Holarctic species living in open habitats. For example, the three-toed woodpecker (Picoides tridactylus) and the winter wren (Troglodytes troglodytes) have divergent Nearctic and Palaearctic mitochondrial DNA clades. Furthermore, in these species, the next closest relative of the Nearctic/Palaearctic sister lineages is the Nearctic clade, suggesting that the Palaearctic may have been colonized from the Nearctic. The aim of this study is to test this pattern of intercontinental divergence and colonization in another Holarctic boreal forest resident , the pine grosbeak (Pinicola enucleator). Location, The Holarctic. Methods, We sequenced the mitochondrial ND2 gene and Z -specific intron 9 of the ACO1 gene for 74 pine grosbeaks collected across the Holarctic. The sequences were used to reconstruct the phylogeographical history of this species using maximum likelihood analysis. Results, We discovered two distinct mitochondrial and Z -specific lineages in the Nearctic and one in the Palaearctic. The two Nearctic mtDNA lineages, one in the northern boreal forest and one in south-western mountain forest, were more closely related to each other than either was to the Palaearctic clade. Two Nearctic Z-chromosome clades were sympatric in the boreal and south-western mountain forests. Unlike the topology of the mtDNA tree, the relationship among the Z-chromosome clades was the same as in the three-toed woodpecker and winter wren [Nearctic (Nearctic, Palaearctic)]. The Palaearctic Z-chromosome clade had much lower genetic diversity and a single-peak mismatch distribution with a mean < 25% of that for either Nearctic region, both of which had ragged mismatch distributions. Main conclusions, Our data suggest that, similar to the other boreal forest species, the pine grosbeak has divergent lineages in each northern continent and could have colonized the Palaearctic from the Nearctic. Compared with many Holarctic birds inhabiting open habitats, boreal forest species appear to be more differentiated, possibly because the boreal forests of the Nearctic and Palaearctic have been isolated since the Pliocene (3.5 Ma). [source] Biogeography of Plagiochila (Hepaticae): natural species groups span several floristic kingdomsJOURNAL OF BIOGEOGRAPHY, Issue 7 2003Henk Groth Abstract Aim This paper presents a synthesis of our recent results regarding the biogeography of Plagiochila using a molecular approach, and documents intercontinental ranges within this largest genus of the hepatics. Methods A maximum likelihood analysis of sixty-one nrITS sequences of Plagiochila was performed and the molecular topology obtained was compared with morphological, phytochemical and geographical data. Results Our molecular data set allowed the identification of eleven Plagiochila sections, the majority of which cover at least two floristic kingdoms. Seven sections have species in Europe (sect. Arrectae, Carringtoniae, Fuscoluteae, Glaucescentes, Plagiochila, Rutilantes, Vagae). Plagiochila species from Atlantic Europe are usually close to or conspecific with neotropical taxa, whereas species widespread in Europe are closely related to Asian ones and not to those in the Neotropics. Plagiochila sect. Arrectae represents a neotropical , Atlantic European clade. The section is not closely related , as has often been suggested , to the morphologically similar sect. Zonatae from Asia and western North America. Sequence data show that the African P. integerrima and the neotropical P. subplana are members of the Asian sect. Cucullatae (sect. Ciliatae, syn. nov.), which becomes pantropical in distribution. An ITS sequence of P. boryana from Uganda confirms the Afro-American range of the primarily neotropical sect. Hylacoetes. Similarities in sporophyte morphology between the sect. Cucullatae and sect. Hylacoetes are the result of parallel evolution. Main conclusions Our results indicate that intercontinental ranges at section and species level are common in Plagiochila. Carl's (1931) subdivision of Plagiochila into sections restricted to one floristic kingdom is outdated. Biogeographical patterns in Plagiochila are not dissimilar to those of other groups of bryophytes but elucidation of the geographical ranges of the taxa requires a molecular approach. Contrary to earlier belief, most Plagiochila species from Atlantic Europe do not have close relatives in Asia but are conspecific with or closely related to species from tropical America. [source] A circular statistical method for extracting rotation measuresMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 2 2001S. Sarala We propose a new method for the extraction of rotation measures from spectral polarization data. The method is based on maximum likelihood analysis and takes into account the circular nature of the polarization data. The method is unbiased and statistically more efficient than the standard ,2 procedure. We also find that the method is computationally much more convenient than the standard ,2 procedure if the number of data points is very large. We find that for most sources the method gives results very close to the standard ,2 minimization procedure. We give results for all the cases for which the method gives significantly different results from ,2 minimization. We also make a ,3 fit to the data in order to extract non-Faraday rotation behaviour for those sources for which a large number of data points are available. [source] Alternative Oxidase (AOX) Genes of African Trypanosomes: Phylogeny and Evolution of AOX and Plastid Terminal Oxidase FamiliesTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2005TAKASHI SUZUKI Abstract. To clarify evolution and phylogenetic relationships of trypanosome alternative oxidase (AOX) molecules, AOX genes (cDNAs) of the African trypanosomes, Trypanosoma congolense and Trypanosoma evansi, were cloned by PCR. Both AOXs possess conserved consensus motifs (-E-, -EXXH-). The putative amino acid sequence of the AOX of T. evansi was exactly the same as that of T. brucei. A protein phylogeny of trypanosome AOXs revealed that three genetically and pathogenically distinct strains of T. congolense are closely related to each other. When all known AOX sequences collected from current databases were analyzed, the common ancestor of these three Trypanosoma species shared a sister-group position to T. brucei/T. evansi. Monophyly of Trypanosoma spp. was clearly supported (100% bootstrap value) with Trypanosoma vivax placed at the most basal position of the Trypanosoma clade. Monophyly of other eukaryotic lineages, terrestrial plants + red algae, Metazoa, diatoms, Alveolata, oomycetes, green algae, and Fungi, was reconstructed in the best AOX tree obtained from maximum likelihood analysis, although some of these clades were not strongly supported. The terrestrial plants + red algae clade showed the closest affinity with an ,-proteobacterium, Novosphingobium aromaticivorans, and the common ancestor of these lineages, was separated from other eukaryotes. Although the root of the AOX subtree was not clearly determined, subsequent phylogenetic analysis of the composite tree for AOX and plastid terminal oxidase (PTOX) demonstrated that PTOX and related cyanobacterial sequences are of a monophyletic origin and their common ancestor is linked to AOX sequences. [source] There are High Levels of Functional and Genetic Diversity in Oxyrrhis marinaTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2005CHRIS D. LOWE Abstract. Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O. marina, we assessed diversity among 11 strains using 5.8S rDNA and ITS sequences. The 5.8S rDNA and ITS regions revealed high divergence between strains: 63.1% between the most diverse. To compare O. marina diversity relative to other alveolates, 18S rDNA sequences for five strains were analysed with sequences from representatives of the major alveolate groups. 18S rDNA also revealed high divergence in O. marina. Additionally, consistent with phylogenies based on protein coding genes, maximum likelihood analysis indicated that O. marina was monophyletic and ancestral to the dinoflagellates. To assess ecophysiological differences, growth rates of seven O. marina strains were measured at 10 salinities (10,55,). Two salinity responses occurred: one group achieved highest growth rates at high salinities; the other grew best at low salinities. There was no clear correlation between molecular, ecophysiological, or geographical differences. However, salinity tolerance was associated with habitat type: intertidal strains grew best at high salinities; open-water strains grew best at low salinities. These data indicate the need to examine many strains of a species in both phylogenetic and ecological studies, especially where key-species are used to model ecological processes. [source] | ||||||||||