The problematic phylogenetic analysis of interlocus heteropolymer isozyme characters: a case study from sea snakes and cobras

1988 ◽  
Vol 66 (12) ◽  
pp. 2628-2633 ◽  
Author(s):  
Robert W. Murphy
Keyword(s):  
Phylogenetic Analysis ◽  
Lactate Dehydrogenase ◽  
Phylogenetic Relationships ◽  
Parallel Evolution ◽  
Taxonomic Group ◽  
Data Sets ◽  
Similar Data ◽  
Isozyme Patterns ◽  
Sea Snakes

Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetramer isozymes are encountered when the observed isozyme patterns are superimposed on a well-corroborated cladogram depicting the phylogenetic relationships of some sea snakes, cobras, and coral snakes. This finding may be common among similar data sets because of parallel evolution and the inability to discern transformation sequences. Thus, the utility of this isozyme character in phylogenetic investigations may be severely limited, depending on the taxonomic group or level of universality being investigated.

scholarly journals A molecular phylogenetic analysis of the genera of fruit doves and allies using dense taxonomic sampling

2019 ◽  
Vol 42 ◽  
pp. 2019001
Author(s):  
Jennifer Nowak ◽  
Andrew Sweet ◽  
Jason Weckstein ◽  
Kevin Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Large Fraction ◽  
Nuclear Gene ◽  
Data Sets ◽  
Foraging Mode ◽  
Biogeographic Patterns ◽  
Reconstruction Methods ◽  
Molecular Phylogenetic ◽  
History Of

Fruit doves and their allies are a diverse group within the pigeon and dove family (Aves: Columbidae). Progress towards subfamilial classification of Columbidae relies on identifying major groups and the phylogenetic relationships within these groups. One such recently proposed group is the Raphinae based on previous evidence that the extinct dodo is potentially within what was formerly recognized as the Treroninae (fruit doves and allies). Although several studies have explored the phylogenetic relationships within Columbidae, most have focused either on broad-scale, familial level relationships or finer scale, species level relationships. Here we use mitochondrial and nuclear gene sequences from a diverse taxonomic sample to identify relationships among the genera and species of fruit doves and their allies. In particular our goal is to identify which of these genera should be included within Raphinae (the name which has taxonomic priority over Treroninae), focusing on an inclusive, well-supported monophyletic group. We also use dense taxon sampling to explore relationships among genera and species in this group, expanding on previous studies. In addition, we use resulting phylogenetic hypotheses to reconstruct the ancestral evolutionary history of foraging mode and biogeographic patterns of dispersal within the group. We used two data sets for our phylogenetic analysis: the first consisting of novel sequences generated for this project and the second with additional, previously published sequences from the fruit dove genus (Ptilinopus). Our analyses found support for the monophyly of a clade that contains a large fraction of the genera currently classified within Raphinae and also found several well-supported clades within this group of pigeons and doves. Character reconstruction methods based on the resulting phylogeny recover multiple transitions from a terrestrial to an arboreal foraging mode and evidence for multiple dispersal events from Asia to Africa throughout the history of the clade.

scholarly journals Phylogenetic Analysis of Mandarin Landraces, Wild Mandarins, and Related Species in China Using Nuclear LEAFY Second Intron and Plastid trnL-trnF Sequence

2007 ◽  
Vol 132 (6) ◽  
pp. 796-806 ◽  
Author(s):  
Li Yingzhi ◽  
Cheng Yunjiang ◽  
Tao Nengguo ◽  
Deng Xiuxin
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Average Length ◽  
Hybrid Origin ◽  
Data Sets ◽  
Citrus Reticulata ◽  
F Region ◽  
Plausible Hypothesis

Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.

scholarly journals Extensive Introgression among Ancestral mtDNA Lineages: Phylogenetic Relationships of the Utaka within the Lake Malawi Cichlid Flock

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Dieter Anseeuw ◽  
Bruno Nevado ◽  
Paul Busselen ◽  
Jos Snoeks ◽  
Erik Verheyen
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Gene Pool ◽  
Nuclear Dna ◽  
Lake Malawi ◽  
The Other ◽  
Taxonomic Group ◽  
Cichlid Species ◽  
Mtdna Lineages ◽  
Hybridisation Event

We present a comprehensive phylogenetic analysis of the Utaka, an informal taxonomic group of cichlid species from Lake Malawi. We analyse both nuclear and mtDNA data from five Utaka species representing two (Copadichromis and Mchenga) of the three genera within Utaka. Within three of the five analysed species we find two very divergent mtDNA lineages. These lineages are widespread and occur sympatrically in conspecific individuals in different areas throughout the lake. In a broader taxonomic context including representatives of the main groups within the Lake Malawi cichlid fauna, we find that one of these lineages clusters within the non-Mbuna mtDNA clade, while the other forms a separate clade stemming from the base of the Malawian cichlid radiation. This second mtDNA lineage was only found in Utaka individuals, mostly within Copadichromis sp. “virginalis kajose” specimens. The nuclear genes analysed, on the other hand, did not show traces of divergence within each species. We suggest that the discrepancy between the mtDNA and the nuclear DNA signatures is best explained by a past hybridisation event by which the mtDNA of another species introgressed into the ancestral Copadichromis sp. “virginalis kajose” gene pool.

scholarly journals Segment-Based Approach for Assessing Hazard Risk of Coastal Highways in Hawai‘i

2019 ◽  
Vol 2673 (1) ◽  
pp. 83-91 ◽  
Author(s):  
Harrison Togia ◽  
Oceana P. Francis ◽  
Karl Kim ◽  
Guohui Zhang
Keyword(s):  
Qualitative Method ◽  
Data Sets ◽  
Regional Environment ◽  
The Road ◽  
Hazard Exposure ◽  
Multiple Indicators ◽  
System Data ◽  
Rural Highway ◽  
Geographic Information System Data

Hazards to roadways and travelers can be drastically different because hazards are largely dependent on the regional environment and climate. This paper describes the development of a qualitative method for assessing infrastructure importance and hazard exposure for rural highway segments in Hawai‘i under different conditions. Multiple indicators of roadway importance are considered, including traffic volume, population served, accessibility, connectivity, reliability, land use, and roadway connection to critical infrastructures, such as hospitals and police stations. The method of evaluating roadway hazards and importance can be tailored to fit different regional hazard scenarios. It assimilates data from diverse sources to estimate risks of disruption. A case study for Highway HI83 in Hawai‘i, which is exposed to multiple hazards, is conducted. Weakening of the road by coastal erosion, inundation from sea level rise, and rockfall hazards require adaptation solutions. By analyzing the risk of disruption to highway segments, adaptation approaches can be prioritized. Using readily available geographic information system data sets for the exposure and impacts of potential hazards, this method could be adapted not only for emergency management but also for planning, design, and engineering of resilient highways.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Queue Length Forecasting in Complex Manufacturing Job Shops

Forecasting ◽  
2021 ◽  
Vol 3 (2) ◽  
pp. 322-338
Author(s):  
Marvin Carl May ◽  
Alexander Albers ◽  
Marc David Fischer ◽  
Florian Mayerhofer ◽  
Louis Schäfer ◽  
...  
Keyword(s):  
Operations Management ◽  
Queue Length ◽  
Manufacturing Systems ◽  
Production Control ◽  
Data Sets ◽  
Job Shops ◽  
Static Data ◽  
Queue Lengths ◽  
Operational Excellence

Currently, manufacturing is characterized by increasing complexity both on the technical and organizational levels. Thus, more complex and intelligent production control methods are developed in order to remain competitive and achieve operational excellence. Operations management described early on the influence among target metrics, such as queuing times, queue length, and production speed. However, accurate predictions of queue lengths have long been overlooked as a means to better understanding manufacturing systems. In order to provide queue length forecasts, this paper introduced a methodology to identify queue lengths in retrospect based on transitional data, as well as a comparison of easy-to-deploy machine learning-based queue forecasting models. Forecasting, based on static data sets, as well as time series models can be shown to be successfully applied in an exemplary semiconductor case study. The main findings concluded that accurate queue length prediction, even with minimal available data, is feasible by applying a variety of techniques, which can enable further research and predictions.

scholarly journals Generalizing Treatment Effect Estimates From Sample to Population: A Case Study in the Difficulties of Finding Sufficient Data

2016 ◽  
Vol 41 (4) ◽  
pp. 357-388 ◽  
Author(s):  
Elizabeth A. Stuart ◽  
Anna Rhodes
Keyword(s):  
Head Start ◽  
Randomized Trial ◽  
Treatment Effect ◽  
External Validity ◽  
Randomized Trials ◽  
Target Population ◽  
Data Sets ◽  
Common Data Elements ◽  
Ex Post

Background: Given increasing concerns about the relevance of research to policy and practice, there is growing interest in assessing and enhancing the external validity of randomized trials: determining how useful a given randomized trial is for informing a policy question for a specific target population. Objectives: This article highlights recent advances in assessing and enhancing external validity, with a focus on the data needed to make ex post statistical adjustments to enhance the applicability of experimental findings to populations potentially different from their study sample. Research design: We use a case study to illustrate how to generalize treatment effect estimates from a randomized trial sample to a target population, in particular comparing the sample of children in a randomized trial of a supplemental program for Head Start centers (the Research-Based, Developmentally Informed study) to the national population of children eligible for Head Start, as represented in the Head Start Impact Study. Results: For this case study, common data elements between the trial sample and population were limited, making reliable generalization from the trial sample to the population challenging. Conclusions: To answer important questions about external validity, more publicly available data are needed. In addition, future studies should make an effort to collect measures similar to those in other data sets. Measure comparability between population data sets and randomized trials that use samples of convenience will greatly enhance the range of research and policy relevant questions that can be answered.

scholarly journals Empirical Underidentification with the Bifactor Model: A Case Study

2017 ◽  
Vol 78 (5) ◽  
pp. 717-736 ◽  
Author(s):  
Samuel Green ◽  
Yanyun Yang
Keyword(s):  
Structural Equation Model ◽  
Structural Equation ◽  
Equation Model ◽  
Bifactor Model ◽  
Data Sets ◽  
Bifactor Models

Bifactor models are commonly used to assess whether psychological and educational constructs underlie a set of measures. We consider empirical underidentification problems that are encountered when fitting particular types of bifactor models to certain types of data sets. The objective of the article was fourfold: (a) to allow readers to gain a better general understanding of issues surrounding empirical identification, (b) to offer insights into empirical underidentification with bifactor models, (c) to inform methodologists who explore bifactor models about empirical underidentification with these models, and (d) to propose strategies for structural equation model users to deal with underidentification problems that can emerge when applying bifactor models.

Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

2005 ◽  
Vol 26 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Francisca do Val ◽  
Paulo Nuin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
The Other ◽  
The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

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