New contributions towards the understanding of the phylogenetic relationships among economically important fruit flies (Diptera: Tephritidae)

2006 ◽  
Vol 96 (3) ◽  
pp. 279-288 ◽  
Author(s):  
M.D. Segura ◽  
C. Callejas ◽  
M.P. Fernández ◽  
M.D. Ochando
Keyword(s):  
Phylogenetic Relationships ◽  
Fruit Flies ◽  
Bactrocera Cucurbitae ◽  
Likelihood Methods ◽  
Morphological Classification ◽  
Important Group ◽  
Tephritid Species ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
The Many

AbstractFruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNASer and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

scholarly journals Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

2019 ◽  
Vol 69 (1) ◽  
pp. 91-109 ◽  
Author(s):  
Marie K Brandrud ◽  
Juliane Baar ◽  
Maria T Lorenzo ◽  
Alexander Athanasiadis ◽  
Richard M Bateman ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Diploid Species ◽  
Climatic Conditions ◽  
Likelihood Methods ◽  
Allopolyploid Speciation ◽  
Naturally Occurring ◽  
Maximum Likelihood Methods ◽  
History Of ◽  
Challenging Situation ◽  
Age Estimates

Abstract Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

scholarly journals Methods for Stratified Cluster Sampling with Informative Stratification

2007 ◽  
Vol 2007 ◽  
pp. 1-12
Author(s):  
Alastair Scott ◽  
Chris Wild
Keyword(s):  
Maximum Likelihood ◽  
Regression Models ◽  
Population Distribution ◽  
Estimating Equation ◽  
Cluster Sampling ◽  
Likelihood Methods ◽  
Weighted Estimating Equation ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Using Data

We look at fitting regression models using data from stratified cluster samples when the strata may depend in some way on the observed responses within clusters. One important subclass of examples is that of family studies in genetic epidemiology, where the probability of selecting a family into the study depends on the incidence of disease within the family. We develop the survey-weighted estimating equation approach for this problem, with particular emphasis on the estimation of superpopulation parameters. Full maximum likelihood for this class of problems involves modelling the population distribution of the covariates which is simply not feasible when there are a large number of potential covariates. We discuss efficient semiparametric maximum likelihood methods in which the covariate distribution is left completely unspecified. We further discuss the relative efficiencies of these two approaches.

A new leaf-litter harvestman species of the genus Karos (Opiliones: Stygnopsidae: Karosinae), with a reanalysis of the morphological phylogeny of the genus

Zootaxa ◽  
2018 ◽  
Vol 4378 (4) ◽  
pp. 533 ◽  
Author(s):  
JESÚS A. CRUZ-LÓPEZ
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Leaf Litter ◽  
Endemic Species ◽  
Sister Group ◽  
Likelihood Methods ◽  
The Family ◽  
Maximum Likelihood Methods

Karos Goodnight & Goodnight, 1944 is the most diverse genus of the family Stygnopsidae. It contains seven micro-endemic species from the Huasteca region in eastern Mexico. In this paper, the new species Karos morronei sp. nov. is described based on the morphology of adults of both sexes. The new species is from Zacualtipán de Ángeles, Hidalgo State, which represents the southernmost record for the genus. Additionally, a reanalysis of the previous morphological phylogeny of the genus using both parsimony and maximum likelihood methods is provided. According to the morphological reanalysis, K. morronei sp. nov. exhibits an autapomorphy (males with femur IV thicker than females) and is the sister group of the clade that includes K. barbarikos, K. hexasetosus, K. monjarazi, K. parvus and K. singularis. Finally, information of barcoding (CO1) is provided for this new species. 

scholarly journals Molecular Phylogeny of the Ant-Decapitating Flies, Genus Apocephalus Coquillett (Diptera: Phoridae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Brian V Brown ◽  
Christine Hayes ◽  
John M Hash ◽  
Paul T Smith
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Likelihood Methods ◽  
Taxonomic Relationships ◽  
Methods Of Analysis ◽  
Maximum Likelihood Methods ◽  
New Synonymy

Abstract The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus. Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.

scholarly journals Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Wanqing Zhao ◽  
Qing Zhao ◽  
Min Li ◽  
Jiufeng Wei ◽  
Xianhong Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Mitochondrial Genomes ◽  
Rna Structures ◽  
Protein Coding ◽  
Transfer Rnas ◽  
The Family ◽  
Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

Systematics of Capparaceae and Cleomaceae: an evaluation of the generic delimitations of Capparis and Cleome using plastid DNA sequence dataThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 682-696 ◽  
Author(s):  
Jocelyn C. Hall
Keyword(s):  
Geographic Distribution ◽  
New World ◽  
Plastid Dna ◽  
Likelihood Methods ◽  
Phylogenetic Reconstructions ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
Taxonomic Implications ◽  
Cleome Arabica ◽  
Selection Of

The phylogenetic relationships in Capparaceae and Cleomaceae were examined using two plastid genes, ndhF and matK, to address outstanding systematic questions in the two families. Specifically, the monophyly of the two type genera, Capparis and Cleome , has recently been questioned. Capparaceae and Cleomaceae were broadly sampled to assess the generic circumscriptions of both genera, which house the majority of species for each family. Phylogenetic reconstructions using maximum parsimony and maximum likelihood methods strongly contradict monophyly for both type genera. Within Capparaceae, Capparis is diphyletic: the sampled species belong to two of the five major lineages recovered in the family, which corresponds with their geographic distribution. One lineage contains all sampled New World Capparis and four other genera ( Atamisquea , Belencita , Morisonia , and Steriphoma ) that are distributed exclusively in the New World. The other lineage contains Capparis species from the Old World and Australasia, as well as the Australian genus, Apophyllum . Species of Cleome are scattered across each of four major lineages identified within Cleomaceae: (i) Cleome in part, Dactylaena , Dipterygium , Gynandropsis , Podandrogyne , and Polanisia ; (ii) Cleome droserifolia (Forssk.) Del.; (iii)  Cleome arabica L., and Cleome ornithopodioides L.; and (iv) Cleome in part, Cleomella , Isomeris , Oxystylis , and Wislizenia . Resolution within and among these major clades of Cleomaceae is limited, and there is no clear correspondence of clades with geographic distribution. Within each family, morphological support and taxonomic implications of the molecular-based clades are discussed.

Phylogenetic relationships among megachiropteran species from the two major islands of the Philippines, deduced from DNA sequences of the cytochrome b gene

2001 ◽  
Vol 79 (9) ◽  
pp. 1671-1677 ◽  
Author(s):  
Severo T Bastian, Jr. ◽  
Kazuaki Tanaka ◽  
Rea Victoria P Anunciado ◽  
Nelson G Natural ◽  
Augusto C Sumalde ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
The Philippines ◽  
Cytochrome B Gene ◽  
Likelihood Methods ◽  
Base Pairs ◽  
Maximum Likelihood Methods ◽  
Pteropus Vampyrus ◽  
Cynopterus Brachyotis

Complete cytochrome b gene sequences (1140 base pairs) in species of Megachiroptera were ascertained in order to deduce their phylogenetic relationships, using samples of Cynopterus brachyotis, Eonycteris spelaea, Ptenochirus jagori, Pteropus vampyrus, and Rousettus amplexicaudatus collected from the islands of Luzon and Mindanao in the Philippines. Genetic divergence between samples of R. amplexicaudatus, E. spelaea, and C. brachyotis was very small. On the other hand, a large genetic distance was detected between species of Megachiroptera. The phylogenetic tree using neighbor-joining, parsimony, and maximum-likelihood methods generated similar topologies, reflecting the evolutionary associations among megachiropteran species. We estimated that Megachiroptera separated from Microchiroptera 50.2 million years ago (MYA), and split further approximately 32.4 MYA, forming three lineages: E. spelaea, R. amplexicaudatus, and P. vampyrus and the P. jagori – C. brachyotis cluster. The third lineage, composed of P. vampyrus and the P. jagori – C. brachyotis cluster, branched out 31.9 MYA. We hypothesize that R. amplexi caudatus diverged from the three members of the subfamily Pteropodinae examined, and its phylogenetic relationship with E. spelaea remains unclear.

scholarly journals Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships

1999 ◽  
Vol 80 (8) ◽  
pp. 2229-2237 ◽  
Author(s):  
Pepito Q. Cabauatan ◽  
Ulrich Melcher ◽  
Koichi Ishikawa ◽  
Toshihiro Omura ◽  
Hiroyuki Hibino ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Open Reading Frames ◽  
Rice Tungro Bacilliform Virus ◽  
Likelihood Methods ◽  
Nucleotide Substitutions ◽  
Rich Region ◽  
Evolutionary Forces ◽  
Maximum Likelihood Methods ◽  
Tree Topologies

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

scholarly journals The evolution of the vestibular apparatus in apes and humans

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Alessandro Urciuoli ◽  
Clément Zanolli ◽  
Amélie Beaudet ◽  
Jean Dumoncel ◽  
Frédéric Santos ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Vestibular Apparatus ◽  
Likelihood Methods ◽  
Geometric Morphometric ◽  
Bony Labyrinth ◽  
Maximum Likelihood Methods ◽  
Geometric Morphometric Analysis ◽  
Fossil Apes

Phylogenetic relationships among extinct hominoids (apes and humans) are controversial due to pervasive homoplasy and the incompleteness of the fossil record. The bony labyrinth might contribute to this debate, as it displays strong phylogenetic signal among other mammals. However, the potential of the vestibular apparatus for phylogenetic reconstruction among fossil apes remains understudied. Here we test and quantify the phylogenetic signal embedded in the vestibular morphology of extant anthropoids (monkeys, apes and humans) and two extinct apes (Oreopithecus and Australopithecus) as captured by a deformation-based 3D geometric morphometric analysis. We also reconstruct the ancestral morphology of various hominoid clades based on phylogenetically-informed maximum likelihood methods. Besides revealing strong phylogenetic signal in the vestibule and enabling the proposal of potential synapomorphies for various hominoid clades, our results confirm the relevance of vestibular morphology for addressing the controversial phylogenetic relationships of fossil apes.

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