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Constructing (Almost) Phylogenetic Trees from Developmental Sequences Data [chapter]

Ronnie Bathoorn, Arno Siebes
2004 Lecture Notes in Computer Science  
Rather than basing the tree on genetic sequence data ours is based on developmental sequence data.  ...  In this paper we present a new way of constructing almost phylogenetic trees. Almost since we reconstruct the tree, but without the timestamps.  ...  sequence data, e.g., for the construction of evolutionary trees.  ... 
doi:10.1007/978-3-540-30116-5_46 fatcat:6rovk5fsbvexbai2ka4dayi3n4

Almost There: Transmission Routes of Bacterial Symbionts between Trophic Levels

Elad Chiel, Einat Zchori-Fein, Moshe Inbar, Yuval Gottlieb, Tetsuya Adachi-Hagimori, Suzanne E. Kelly, Mark K. Asplen, Martha S. Hunter, Jason E. Stajich
2009 PLoS ONE  
Horizontal transmission has been mostly inferred from phylogenetic studies but the mechanisms of spread are still largely a mystery.  ...  Here, we investigated transmission of two distantly related bacterial symbionts -Rickettsia and Hamiltonella -from their host, the sweet potato whitefly, Bemisia tabaci, to three species of whitefly parasitoids  ...  We would also like to thank four anonymous reviewers for their very constructive comments on the manuscript. Author Contributions  ... 
doi:10.1371/journal.pone.0004767 pmid:19274091 pmcid:PMC2651630 fatcat:2ex5bvw4mbhevphs2azfkheedq

EVOLUTIONARY-DEVELOPMENTAL CHANGE IN THE GROWTH ARCHITECTURE OF FOSSIL RHIZOMORPHIC LYCOPSIDS: SCENARIOS CONSTRUCTED ON CLADISTIC FOUNDATIONS

RICHARD M. BATEMAN
1994 Biological Reviews  
Tribal relationships in Onagraceae: implications from rbcL sequence data. Annals of the Missouri Botanical Garden 80, 672-685. Corner, E. J. H. (1949).  ...  As phylogenetic indicators, nucleic acid sequences offer the opportunity of testing hypotheses based on phenotypic data; they would, for example, be particularly valuable to test the hypothesis of reduced  ... 
doi:10.1111/j.1469-185x.1994.tb01249.x fatcat:2eboc7yu2jhkpgsqjbtlqfft4y

Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases

Pei-Jian Cao, Laura E. Bartley, Ki-Hong Jung, Pamela C. Ronald
2008 Molecular Plant  
Through the database, several classes of functional genomic data, including mutant lines and gene expression data, can be displayed for each rice GT in the context of a phylogenetic tree, allowing for  ...  Comprehensive digital expression analysis of public gene expression data revealed that most (;80%) rice GTs are expressed.  ...  Using the neighbor-joining method, we then constructed unrooted phylogenetic trees based on GT domain sequences for each GT family or subfamily with more than three members.  ... 
doi:10.1093/mp/ssn052 pmid:19825588 fatcat:ycfppwjd4nbxtdh4wdeopothui

Do constructional constraints influence cyprinid (Cyprinidae: Leuciscinae) craniofacial coevolution?

C. DARRIN HULSEY, PHILLIP R. HOLLINGSWORTH JR
2011 Biological Journal of the Linnean Society  
For example, evolutionary trade-offs resulting from limited space in the head could have influenced how the sizes of the jaw muscle, as well as the eyes, evolved in North American cyprinid fishes.  ...  However, there was a negative relationship between mass of adductor mandibulae 1 and eye volume, indicating that change in these physically adjacent structures is consistent with an evolutionary constructional  ...  GenBank sequences from Danio rerio and novel sequences of the catastomid Catostomus commersoni were included as outgroups in the phylogenetic analysis.  ... 
doi:10.1111/j.1095-8312.2011.01628.x fatcat:ugwf4wdqrbdsbnuldqgqfd2q6e

A HindIII BAC library construction of Mesobuthus martensii Karsch (Scorpiones:Buthidae): An important genetic resource for comparative genomics and phylogenetic analysis

Songryong Li, Yibao Ma, Shenghun Jang, Yingliang Wu, Hui Liu, Zhijian Cao, Wenxin Li
2009 Genes & Genetic Systems  
phylogenetic analysis.  ...  a HindIII BAC library of the male scorpion M. martensii Karsch from China.  ...  The phylogenetic trees resulting from NJ and MP analyses based on 18S rDNA sequences, with Calocheiridius cf. termitophilus (Arachnida: Pseudoscorpiones, GenBank accession no.  ... 
doi:10.1266/ggs.84.417 pmid:20228579 fatcat:gsorcpt6z5a27gl4pnmz4qjbre

The construction of an EST database for Bombyx mori and its application

K. Mita, M. Morimyo, K. Okano, Y. Koike, J. Nohata, H. Kawasaki, K. Kadono-Okuda, K. Yamamoto, M. G. Suzuki, T. Shimada, M. R. Goldsmith, S. Maeda
2003 Proceedings of the National Academy of Sciences of the United States of America  
Because gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the  ...  To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database.  ...  Sequence data from this article have been deposited in DDBJ (DNA Data Bank of Japan) under accession numbers shown in Table 1 . Clones can be obtained by contacting K.M. cDNA Libraries.  ... 
doi:10.1073/pnas.2234984100 pmid:14614147 pmcid:PMC283556 fatcat:5vvnkwoq4bfd5hpqz3zmq66fdm

Construction, database integration, and application of an Oenothera EST library

Jaroslav Mráček, Stephan Greiner, Won Kyong Cho, Uwe Rauwolf, Martha Braun, Pavan Umate, Johannes Altstätter, Rhea Stoppel, Lada Mlčochová, Martina V. Silber, Stefanie M. Volz, Sarah White (+4 others)
2006 Genomics  
An integrated approach involving cDNA cloning, EST sequencing, and bioinformatic data mining was chosen using Oenothera elata with the genetic constitution nuclear genome AA with plastome type I.  ...  Coevolution of cellular genetic compartments is a fundamental aspect in eukaryotic genome evolution that becomes apparent in serious developmental disturbances after interspecific organelle exchanges.  ...  sequenced from their 5′ ends.  ... 
doi:10.1016/j.ygeno.2006.05.010 pmid:16829020 fatcat:4izof5jfqvdjrbr7irgvelvwve

Origin of the holothurians (Echinodermata) derived by constructional morphology

R. Haude
2002 Fossil Record  
n. gen., n. sp.) obviously corroborate homology of holothurian and other echinoderm radial systems; (v) different extent of podial and body wall skeletonization suggests the existence of respiratory trees  ...  Following results are discussed: (i) Holothurians have to be derived from a postlarval precursor; (ii) "Apodida" (as molecular-genetically derived first holothurians) must originally have been pedate;  ...  are presented as the only reliable scientific fundament; (ii) belief in sequencing data reflects hope that regulator gene analysis would solve morphological problems ; and (iii) by ignoring the physical  ... 
doi:10.5194/fr-5-141-2002 fatcat:mpdx2qbukzdrzijrvk6p22rpeu

Apolipophorin-II/I Contributes to Cuticular Hydrocarbon Transport and Cuticle Barrier Construction in Locusta migratoria

Yiyan Zhao, Weimin Liu, Xiaoming Zhao, Zhitao Yu, Hongfang Guo, Yang Yang, Jianqin Zhang, Bernard Moussian, Jianzhen Zhang
2020 Frontiers in Physiology  
Apolipophorins are carrier proteins that bind lipids and mediate their transport from tissue to tissue in animals. Apolipophorin I and II (apoLp-II/I) are the major apolipophorins in insects.  ...  Construction of Phylogenetic Tree A phylogenetic analysis of apoLp-II/I was performed by using the full-length amino acid sequences of representative apoLp-II/I proteins in different insects such as Blattella  ...  The GenBank accession numbers of apoLp-II/I from the different species used to construct the phylogenetic tree are listed in Supplementary Table S1 .  ... 
doi:10.3389/fphys.2020.00790 pmid:32733279 pmcid:PMC7360829 fatcat:fgfegzo24zbepgjvkmzg6g5khm

Race as Social Construct

Helmuth Nyborg
2019 Psych  
It is often claimed that race is a social construct and that scientists studying race differences are disruptive racists.  ...  formalism, each of the claims is found theoretically and empirically unsustainable, as Morton's continuously evolving race position is misrepresented, race relates significantly to geography, we are far from  ...  Acknowledgments: The many constructive and critical comments from the anonymous reviewers are gratefully acknowledged. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/psych1010011 fatcat:m5bokgcb7fgwxpr4hrsdlwdima

Construction and Characterization of Normalized cDNA Libraries by 454 Pyrosequencing and Estimation of DNA Methylation Levels in Three Distantly Related Termite Species

Yoshinobu Hayashi, Shuji Shigenobu, Dai Watanabe, Kouhei Toga, Ryota Saiki, Keisuke Shimada, Thomas Bourguignon, Nathan Lo, Masaru Hojo, Kiyoto Maekawa, Toru Miura, Ken Mills
2013 PLoS ONE  
We generated normalized cDNA libraries from whole bodies, except for guts containing microbes, of almost all castes, sexes and developmental stages and sequenced them with the 454 GS FLX titanium system  ...  To facilitate future molecular studies, we aimed to construct expressed sequence tag (EST) libraries covering wide ranges of gene repertoires in three representative termite species, Hodotermopsis sjostedti  ...  N. takasagoensis is at the most apical part in the termite phylogenetic tree [18] .  ... 
doi:10.1371/journal.pone.0076678 pmid:24098800 pmcid:PMC3787108 fatcat:pzouyym3d5bltpglgheunppgfu

MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants

K.-U. Winter, A. Becker, T. Munster, J. T. Kim, H. Saedler, G. Theissen
1999 Proceedings of the National Academy of Sciences of the United States of America  
Most phylogenetic analyses based on morphological data agree that among the groups of extant seed plants, the gnetophytes are the sister group of the angiosperms.  ...  This provides strong molecular evidence for a sister-group relationship between gnetophytes and conifers, which is in contradiction to widely accepted interpretations of morphological data for almost a  ...  We also thank the Automatic DNA Isolation and Sequencing team of our institute for sequencing the cDNA clones.  ... 
doi:10.1073/pnas.96.13.7342 pmid:10377416 pmcid:PMC22087 fatcat:mu7ifn243jcwtnhiedztd6dl5e

Luciferins Under Construction: A Review of Known Biosynthetic Pathways

Aleksandra S. Tsarkova
2021 Frontiers in Ecology and Evolution  
This advantageous trait has independently evolved dozens of times, with current estimates ranging from the most conservative 40, based on the biochemical diversity found across bioluminescence systems  ...  marked by extraordinary discoveries and promising breakthroughs in understanding the molecular basis of multiple bioluminescence systems, the mechanisms of luciferin biosynthesis for many organisms remain almost  ...  A recent study employing metagenomic data analysis revealed a much wider diversity of lux operon sequences organization with novel lux genes and operons being more abundant in the global ocean than the  ... 
doi:10.3389/fevo.2021.667829 fatcat:dee4663r6bbrbpc5bhynnwpgwu

HETEROCHRONIC VARIATION IN THE DEVELOPMENTAL TIMING OF CRANIAL OSSIFICATIONS IN POECILIID FISHES (CYPRINODONTIFORMES)

Richard E. Strauss
1990 Evolution  
The timing profiles by themselves, when used to construct hypothetical phylogenetic trees, contain sufficient historical information to recover evolutionary relationships consistent with conventional systematic  ...  To the extent that such sequences are evolutionarily conservative, they may also provide a basis for phylogenetic inference.  ...  Rather than assuming these developmental events to be evolutionarily independent, we may estimate their phylogenetic correlations by mapping the events onto a phylogenetic tree derived independently from  ... 
doi:10.1111/j.1558-5646.1990.tb03846.x pmid:28564319 fatcat:5hdeaome3zhnja2swkv6q2fize
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