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Phylogenetic and Mechanistic Analysis of A Developmentally Integrated Character Complex: Alternate Life History Modes in Ambystomatid Salamanders1

1996 American Zoologist  
Many of the critical pieces are now in place to exploit the evolution of paedomorphosis (metamorphic failure) as a model for both the phylogenetic and mechanistic analysis of a developmentally integrated  ...  We provide an overview of the genetic strategies that we are using toward this end, and present some of our own published and unpublished results.  ...  One strategy for answering these questions is to use a model system in which both the evolutionary history and mechanistic basis of character variation can be traced during the course of phylogenetic history  ... 
doi:10.1093/icb/36.1.24 fatcat:36ytojtsyrfvxfsjqymmbzvxxi

Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude

Qingle Cai, Xiaoju Qian, Yongshan Lang, Yadan Luo, Jiaohui Xu, Shengkai Pan, Yuanyuan Hui, Caiyun Gou, Yue Cai, Meirong Hao, Jinyang Zhao, Songbo Wang (+7 others)
2013 Genome Biology  
The phylogeny of the ground tit is also controversial. Results: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit.  ...  Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family.  ...  Acknowledgements We thank Dr Fumin Lei and Dr Laurie Goodman for help in revising the manuscript. Authors' details  ... 
doi:10.1186/gb-2013-14-3-r29 pmid:23537097 pmcid:PMC4053790 fatcat:en2xd6pv3fgf5kkcwdi5dftpa4

The evolution of reproductive and genomic diversity in ray-finned fishes: insights from phylogeny and comparative analysis

J. E. Mank, J. C. Avise
2006 Journal of Fish Biology  
Each column in the matrix represents a monophyletic clade from a source phylogeny, dichotomously coded for presence (1) or absence (0) of a taxon in a given clade. 4  ...  In many cases, repeated independent origins of complex reproductive strategies have been uncovered, probably reflecting convergent selection operating on common suites of underlying genes and hormonal  ...  Bryne, A. Tatarenkov and two anonymous reviewers for their helpful comments.  ... 
doi:10.1111/j.1095-8649.2006.01132.x fatcat:fuutjbg2vncg3fojbs62rjeuvy

A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family

M. Li
1998 Journal of Endocrinology  
On the basis of nucleotide sequences of the coding region and their predicted amino acid sequences, 58 glycoprotein hormone subunit genes were compared, aligned and used to construct phylogenetic trees  ...  In addition, on the basis of results from this and other studies, we propose an evolutionary history for this glycoprotein hormone family.  ...  Acknowledgements The authors thank Dr T A Farmerie of Case Western Reserve University School of Medicine for providing the horse -subunit nucleotide sequence and Dr J Felsenstein for providing the PHYLIP  ... 
doi:10.1677/joe.0.1560529 pmid:9582510 fatcat:nnj7kivvefhuto6c5okbku6mrq

Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference

Charles Pugh, Oralia Kolaczkowski, Austin Manny, Bryan Korithoski, Bryan Kolaczkowski
2016 BMC Evolutionary Biology  
Results: Using kinetic binding assays and molecular dynamics simulations of ancestral proteins, we demonstrate how a small number of adaptive protein-coding changes repeatedly shifted the RNA preference  ...  Although resurrecting ancestral proteins is a powerful tool for understanding the molecularfunctional evolution of gene families, nearly all studies have examined proteins functioning in relatively stable  ...  Consent for publication This study does not involve human subject data and therefore does not require informed consent to publish.  ... 
doi:10.1186/s12862-016-0818-6 pmid:27825296 pmcid:PMC5101713 fatcat:2q4iwvey7rdnbfcjv3ddxzb4su

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

David A. Baltrus, Marc T. Nishimura, Artur Romanchuk, Jeff H. Chang, M. Shahid Mukhtar, Karen Cherkis, Jeff Roach, Sarah R. Grant, Corbin D. Jones, Jeffery L. Dangl, David S. Guttman
2011 PLoS Pathogens  
This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pangenome of the species.  ...  These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens.  ...  For both parsimony and maximum likelihood, a consensus tree was created from 100 independent phylogenies.  ... 
doi:10.1371/journal.ppat.1002132 pmid:21799664 pmcid:PMC3136466 fatcat:gfswixcv5vhfrhlavxgd32uwua

Comprehensive Analysis and Expression Profiling of PIN, AUX/LAX, and ABCB Auxin Transporter Gene Families in Solanum tuberosum under Phytohormone Stimuli and Abiotic Stresses

Chenghui Yang, Dongdong Wang, Chao Zhang, Minghui Ye, Nana Kong, Haoli Ma, Qin Chen
2021 Biology  
A large number of auxin-responsive and stress-related cis-elements within their promoters could account for their responsiveness to diverse stresses.  ...  Here, we conducted a comprehensive analysis of auxin transporter gene families in potato to examine genomic distributions, phylogeny, co-expression analysis, gene structure and subcellular localization  ...  Acknowledgments: The authors would like to acknowledge Gang Li (Department of Biological Repositories, Zhongnan Hospital of Wuhan University) for providing technical assistance to us.  ... 
doi:10.3390/biology10020127 pmid:33562678 pmcid:PMC7915614 fatcat:jgplfsh42zgidb7eol64c6zpr4

Defining genetic intra-tumor heterogeneity: a chronological annotation of mutational pathways

Wentao Luo, Fan Wu, Susan R Atlas, Gavin Pickett, Kimberly K Leslie, Donghai Dai
2010 Proceedings in Obstetrics and Gynecology  
These studies will enable us to investigate consistency and stability across alternative reconstructed clonal phylogenies and develop a final consensus reconstruction for the given set of clones, including  ...  Since our aim in the present study is to lustrate a general experimental/modeling ced a new oncept in cancer biology: a temporal il strategy for the reconstruction of cancer clone genealogies, Fig. 3  ... 
doi:10.17077/2154-4751.1008 fatcat:jnj64emvkjhudawlpzssrdgz6y

Portrait of a genus: the genetic diversity of Zea [article]

Lu Chen, Jingyun Luo, Minliang Jin, Ning Yang, Xiangguo Liu, Yong Peng, Wenqiang Li, Liu Qing, Yuejia Yin, Xinnan Ye, Jiali Yan, Qinghua Zhang (+17 others)
2021 bioRxiv   pre-print
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms.  ...  This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in  ...  Whole genome scanning for regions of teosinte elevation adaptation and maize temperate adaptation was implemented by a mixed method.  ... 
doi:10.1101/2021.04.07.438828 fatcat:f4xqdjwmsrcv5prevu2i4ijtyi

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

Li Yi, Menggen Dalai, Rina Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
2020 BMC Genomics  
Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp.  ...  Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments.  ...  Authors' contributions LY, MD and RNS contributed equally to this work as first authors, wrote the manuscript, made substantial contributions to acquisition of data and analysis, interpretation of data  ... 
doi:10.1186/s12864-020-6495-2 pmid:32005147 pmcid:PMC6995116 fatcat:zbqkn5airbappfvviw4hmskt24

Comparative Genomics of Taphrina Fungi Causing Varying Degrees of Tumorous Deformity in Plants

Isheng J. Tsai, Eiji Tanaka, Hayato Masuya, Ryusei Tanaka, Yuuri Hirooka, Rikiya Endoh, Norio Sahashi, Taisei Kikuchi
2014 Genome Biology and Evolution  
The genomes provide a rich resource for investigation into Taphrina biology and evolutionary studies across the basal ascomycetes clade.  ...  High levels of gene synteny within Taphrina species were observed, and our comparative analysis further revealed that these fungi may utilize multiple strategies in coping with the host environment that  ...  Acknowledgments The authors thank John Jones, Daryi Wang, Tzi-Yuan Wang, Yoshitaka Takano, and Anna Avrova for reading and commenting the manuscript, Masabumi Komatsu and Yu Ichihara for providing fungal  ... 
doi:10.1093/gbe/evu067 pmid:24682155 pmcid:PMC4007546 fatcat:7lwshjmr7vek3ek4d3gvmevp4u

A Caenorhabditis motif compendium for studying transcriptional gene regulation

Christoph Dieterich, Ralf J Sommer
2008 BMC Genomics  
A comprehensive parts list of putative regulatory motifs was yet missing for this model system.  ...  The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multicellular organisms.  ...  Acknowledgements We thank Adrian Streit and Benjamin Schlager for valuable discussions. We also thank Michael Han for sharing a script to display multiple alignments.  ... 
doi:10.1186/1471-2164-9-30 pmid:18215260 pmcid:PMC2248174 fatcat:nwqd2typunccbi2guf2b5iair4

Large-Scale Transcriptome Analysis of Retroelements in the Migratory Locust, Locusta migratoria

Feng Jiang, Meiling Yang, Wei Guo, Xianhui Wang, Le Kang, Jialin Charles Zheng
2012 PLoS ONE  
A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified.  ...  The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements.  ...  Acknowledgments We gratefully acknowledge Xiaoxue Zhang for polishing the manuscript and Yanli Wang for assistance in DNA sequencing.  ... 
doi:10.1371/journal.pone.0040532 pmid:22792363 pmcid:PMC3391268 fatcat:dvm36vqrbbfqvgx3wzv2uqxwsi

Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

Mehanathan Muthamilarasan, Venkata S. Bonthala, Rohit Khandelwal, Jananee Jaishankar, Shweta Shweta, Kashif Nawaz, Manoj Prasad
2015 Frontiers in Plant Science  
of SiWRKY066 and SiWRKY082 in stress and hormone signaling.  ...  Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement  ...  Expression Pattern of SiWRKY Genes in Response to Stress and Hormone Treatments To investigate the expression of SiWRKY genes in response to abiotic stress and hormone treatments, 12 genes were selected  ... 
doi:10.3389/fpls.2015.00910 pmid:26635818 pmcid:PMC4654423 fatcat:5z2vuxovz5etbktbftdw5ul7cy

Genome of octoploid plant maca (Lepidium meyenii) illuminates genomic basis for high altitude adaptation in the central Andes [article]

Jun Sheng, Wei Chen, Yang Dong, Liangsheng Zhang, Jing Zhang, Yang Tian, Liang Yan, Guanghui Zhang, Xiao Wang, Yan Zeng, Jiajin Zhang, Xiao Ma (+8 others)
2015 bioRxiv   pre-print
Comparative genomics between maca and close-related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway and secondary  ...  Retention and subsequent evolution of many duplicated genes may account for the morphological and physiological changes (i.e. small leaf shape and loss of vernalization) in maca for high altitude environment  ...  A second evolutionary model with yeast, however, concluded that duplication of a whole pathway was necessary for DNA library construction and sequencing Genomic DNA was extracted and then fragmented  ... 
doi:10.1101/017590 fatcat:do4zvhpfkzddnl2aw4jrxs4p4i
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