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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 1 of 10

  1. The Cyanidiophyceae is an early-diverged red algal class that thrives in extreme conditions around acidic hot springs. Although this lineage has been highlighted as a model for understanding the biology of ext...

    Authors: Chung Hyun Cho, Seung In Park, Claudia Ciniglia, Eun Chan Yang, Louis Graf, Debashish Bhattacharya and Hwan Su Yoon

    Citation: BMC Evolutionary Biology 2020 20:112

    Content type: Research article

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  2. For decades, codon usage has been used as a measure of adaptation for translational efficiency and translation accuracy of a gene’s coding sequence. These patterns of codon usage reflect both the selective and...

    Authors: Cedric Landerer, Brian C. O’Meara, Russell Zaretzki and Michael A. Gilchrist

    Citation: BMC Evolutionary Biology 2020 20:109

    Content type: Research article

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  3. Distant hybridization between the sea urchin Heliocidaris crassispina (♀) and the sea urchin Strongylocentrotus intermedius (♂) was successfully performed under laboratory conditions. A new variety of hybrid sea ...

    Authors: Yaoyao Zhan, Jingxian Sun, Yingying Li, Dongyao Cui, Weijie Zhang, Limeng Yang and Yaqing Chang

    Citation: BMC Evolutionary Biology 2020 20:101

    Content type: Research article

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  4. Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent) amino acid substitutions in proteins ...

    Authors: Samuel H. A. von der Dunk and Berend Snel

    Citation: BMC Evolutionary Biology 2020 20:98

    Content type: Research article

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  5. Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation...

    Authors: Wenpan Dong, Chao Xu, Jun Wen and Shiliang Zhou

    Citation: BMC Evolutionary Biology 2020 20:96

    Content type: Research article

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  6. The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of t...

    Authors: Zhengquan Zhang, Jianzhou Qu, Feifei Li, Silu Li, Shutu Xu, Renhe Zhang, Jiquan Xue and Dongwei Guo

    Citation: BMC Evolutionary Biology 2020 20:91

    Content type: Research article

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  7. ATP-binding cassette (ABC) transporters are involved in the active transportation of various endogenous or exogenous substances. Two ABCG2 gene subfamily members have been identified in birds. A detailed comparat...

    Authors: Shengchao Ma, Hehe Liu, Wenqiang Sun, Ahsan Mustafa, Yang Xi, Fajun Pu, Yanying Li, Chunchun Han, Lili Bai and He Hua

    Citation: BMC Evolutionary Biology 2020 20:85

    Content type: Research article

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  8. Small leucine-rich repeat protein (SLRP) family members contain conserved leucine-rich repeat motifs flanked by highly variable N- and C-terminal regions. Most class II and III SLRPs have tyrosine-rich N-termi...

    Authors: Morten M. Jensen and Henrik Karring

    Citation: BMC Evolutionary Biology 2020 20:73

    Content type: Research article

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  9. Lipids contained in milk are an essential source of energy and structural materials for a growing neonate. Furthermore, lipids’ long-chain unsaturated fatty acid residues can directly participate in neonatal t...

    Authors: Aleksandra Mitina, Pavel Mazin, Anna Vanyushkina, Nikolay Anikanov, Waltraud Mair, Song Guo and Philipp Khaitovich

    Citation: BMC Evolutionary Biology 2020 20:70

    Content type: Research article

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  10. Cysteine-RIch Secretory Proteins (CRISP) are expressed in the reproductive tract of mammalian males and are involved in fertilization and related processes. Due to their important role in sperm performance and...

    Authors: Lena Arévalo, Nicolás G. Brukman, Patricia S. Cuasnicú and Eduardo R. S. Roldan

    Citation: BMC Evolutionary Biology 2020 20:67

    Content type: Research article

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  11. Functional constraint through genomic architecture is suggested to be an important dimension of genome evolution, but quantitative evidence for this idea is rare. In this contribution, existing evidence and di...

    Authors: Katharina C. Wollenberg Valero

    Citation: BMC Evolutionary Biology 2020 20:58

    Content type: Research article

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  12. Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial ...

    Authors: Huihui Chang, Yimeng Nie, Nan Zhang, Xue Zhang, Huimin Sun, Ying Mao, Zhongying Qiu and Yuan Huang

    Citation: BMC Evolutionary Biology 2020 20:57

    Content type: Research article

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  13. Amylase gene clusters have been implicated in adaptive copy number changes in response to the amount of starch in the diet of humans and mammals. However, this interpretation has been questioned for humans and...

    Authors: Miriam Linnenbrink, Kristian K. Ullrich, Ellen McConnell and Diethard Tautz

    Citation: BMC Evolutionary Biology 2020 20:56

    Content type: Research article

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  14. Meiosis is essential for sexual reproduction and generates genetically diverse haploid gametes from a diploid germ cell. Reduction of ploidy depends on active chromosome movements during early meiotic prophase...

    Authors: Irene da Cruz, Céline Brochier-Armanet and Ricardo Benavente

    Citation: BMC Evolutionary Biology 2020 20:55

    Content type: Research article

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  15. Raw second-generation (2G) lignocellulosic biomass materials have the potential for development into a sustainable and renewable source of energy. Poplar is regarded as a promising 2G material (P. davidiana Dode×...

    Authors: Xin Zhang, Chenrui Gu, Tianxu Zhang, Botong Tong, Heng Zhang, Yueliang Wu and Chuanping Yang

    Citation: BMC Evolutionary Biology 2020 20:51

    Content type: Research article

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  16. Parasites may mediate the success of biological invasions through their effect on host fitness and thus, on host population growth and stability. However, a release from the pressure of parasites is strongly r...

    Authors: Aleksandra Biedrzycka, Marcin Popiołek and Andrzej Zalewski

    Citation: BMC Evolutionary Biology 2020 20:43

    Content type: Research article

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  17. Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion...

    Authors: Tsviya Olender, Tamsin E. M. Jones, Elspeth Bruford and Doron Lancet

    Citation: BMC Evolutionary Biology 2020 20:42

    Content type: Methodology article

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  18. Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chro...

    Authors: R. Alan Harris, Muthuswamy Raveendran, Kim C. Worley and Jeffrey Rogers

    Citation: BMC Evolutionary Biology 2020 20:33

    Content type: Research article

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  19. Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is possible t...

    Authors: David E. Northover, Stephen D. Shank and David A. Liberles

    Citation: BMC Evolutionary Biology 2020 20:24

    Content type: Research article

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  20. Drosophila subobscura exhibits a rich inversion polymorphism, with some adaptive inversions showing repeatable spatiotemporal patterns in frequencies related to temperature. Previous studies reported increased ba...

    Authors: Marta Puig Giribets, Mauro Santos and María Pilar García Guerreiro

    Citation: BMC Evolutionary Biology 2020 20:17

    Content type: Research article

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  21. The CO2-concentrating mechanism associated to Crassulacean acid metabolism (CAM) alters the catalytic context for Rubisco by increasing CO2 availability and provides an advantage in particular ecological conditio...

    Authors: Carmen Hermida-Carrera, Mario A. Fares, Marcel Font-Carrascosa, Maxim V. Kapralov, Marcus A. Koch, Arnau Mir, Arántzazu Molins, Miquel Ribas-Carbó, Jairo Rocha and Jeroni Galmés

    Citation: BMC Evolutionary Biology 2020 20:11

    Content type: Research article

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  22. Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been gen...

    Authors: Sheng-Long Kan, Ting-Ting Shen, Ping Gong, Jin-Hua Ran and Xiao-Quan Wang

    Citation: BMC Evolutionary Biology 2020 20:10

    Content type: Research article

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  23. The relative influence of diet and phylogeny on snake venom activity is a poorly understood aspect of snake venom evolution. We measured the activity of two enzyme toxin groups – phospholipase A2 (PLA2), and L-am...

    Authors: Theo Tasoulis, Michael S. Y. Lee, Manon Ziajko, Nathan Dunstan, Joanna Sumner and Geoffrey K. Isbister

    Citation: BMC Evolutionary Biology 2020 20:9

    Content type: Research article

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  24. Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly unipa...

    Authors: Davide Guerra, Manuel Lopes-Lima, Elsa Froufe, Han Ming Gan, Paz Ondina, Rafaela Amaro, Michael W. Klunzinger, Claudia Callil, Vincent Prié, Arthur E. Bogan, Donald T. Stewart and Sophie Breton

    Citation: BMC Evolutionary Biology 2019 19:229

    Content type: Research article

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  25. Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, ...

    Authors: Ana Pinheiro, Ana Águeda-Pinto, José Melo-Ferreira, Fabiana Neves, Joana Abrantes and Pedro J. Esteves

    Citation: BMC Evolutionary Biology 2019 19:221

    Content type: Research article

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  26. Lymphotoxin-α (LTα), located in the Major Histocompatibility Complex (MHC) class III region on chromosome 6, encodes a cytotoxic protein that mediates a variety of antiviral responses among other biological funct...

    Authors: Michael C. Campbell, Bryan Ashong, Shaolei Teng, Jayla Harvey and Christopher N. Cross

    Citation: BMC Evolutionary Biology 2019 19:218

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Evolutionary Biology 2019 19:225

  27. In mammals, the natriuretic system contains three natriuretic peptides, NPPA, NPPB and NPPC, that bind to three transmembrane receptors, NPR1, NPR2 and NPR3. The natriuretic peptides are known only in vertebra...

    Authors: Anna Grandchamp, Shifa Tahir and Philippe Monget

    Citation: BMC Evolutionary Biology 2019 19:215

    Content type: Research article

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  28. The buffalo, despite its superior milk-producing ability, suffers from reproductive limitations that constrain its lifetime productivity. Male sub-fertility, manifested as low conception rates (CRs), is a majo...

    Authors: Vipul Batra, Avinash Maheshwarappa, Komal Dagar, Sandeep Kumar, Apoorva Soni, A. Kumaresan, Rakesh Kumar and T. K. Datta

    Citation: BMC Evolutionary Biology 2019 19:214

    Content type: Research article

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  29. Various apolipoproteins widely distributed among vertebrata play key roles in lipid metabolism and have a direct correlation with human diseases as diagnostic markers. However, the evolutionary progress of apo...

    Authors: Jia-Qian Liu, Wen-Xing Li, Jun-Juan Zheng, Qing-Nan Tian, Jing-Fei Huang and Shao-Xing Dai

    Citation: BMC Evolutionary Biology 2019 19:209

    Content type: Research article

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  30. The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our pr...

    Authors: Hyeon-Mu Cho, Sang-Je Park, Se-Hee Choe, Ja-Rang Lee, Sun-Uk Kim, Yeung-Bae Jin, Ji-Su Kim, Sang-Rae Lee, Young-Hyun Kim and Jae-Won Huh

    Citation: BMC Evolutionary Biology 2019 19:196

    Content type: Research article

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  31. The transition from land to sea by the ancestor of cetaceans approximately 50 million years ago was an incredible evolutionary event that led to a series of morphological, physiological, and behavioral adaptat...

    Authors: Di Sun, Xuming Zhou, Zhenpeng Yu, Shixia Xu, Inge Seim and Guang Yang

    Citation: BMC Evolutionary Biology 2019 19:194

    Content type: Research article

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  32. Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew severely affects yield security wheat production in China. Understanding the virulence structure and genetic variations of this pat...

    Authors: Xian Xin Wu, Xiao Feng Xu, De Xin Ma, Rong Zhen Chen, Tian Ya Li and Yuan Yin Cao

    Citation: BMC Evolutionary Biology 2019 19:183

    Content type: Research article

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  33. Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on ...

    Authors: Juan A. Subirana and Xavier Messeguer

    Citation: BMC Evolutionary Biology 2019 19:181

    Content type: Research article

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  34. Vomeronasal type 1 receptor genes (V1Rs) are expected to detect intraspecific pheromones. It is believed that rodents rely heavily on pheromonal communication mediated by V1Rs, but pheromonal signals are thought ...

    Authors: Hengwu Jiao, Wei Hong, Eviatar Nevo, Kexin Li and Huabin Zhao

    Citation: BMC Evolutionary Biology 2019 19:176

    Content type: Research article

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  35. A number of non-visual responses to light in vertebrates, such as circadian rhythm control and pupillary light reflex, are mediated by melanopsins, G-protein coupled membrane receptors, conjugated to a retinal...

    Authors: Einat Hauzman, Venkatasushma Kalava, Daniela Maria Oliveira Bonci and Dora Fix Ventura

    Citation: BMC Evolutionary Biology 2019 19:174

    Content type: Research article

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  36. In the absence of sex and recombination, genomes are expected to accumulate deleterious mutations via an irreversible process known as Muller’s ratchet, especially in the case of polyploidy. In contrast, no ge...

    Authors: Ladislav Hodač, Simone Klatt, Diego Hojsgaard, Timothy F. Sharbel and Elvira Hörandl

    Citation: BMC Evolutionary Biology 2019 19:170

    Content type: Research article

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  37. Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid...

    Authors: Andrew J. Hudson, David C. McWatters, Bradley A. Bowser, Ashley N. Moore, Graham E. Larue, Scott W. Roy and Anthony G. Russell

    Citation: BMC Evolutionary Biology 2019 19:162

    Content type: Research article

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  38. The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. This evolutionary process can be studied by comparing closel...

    Authors: Henri van Kruistum, Joost van den Heuvel, Joseph Travis, Ken Kraaijeveld, Bas J. Zwaan, Martien A. M. Groenen, Hendrik-Jan Megens and Bart J. A. Pollux

    Citation: BMC Evolutionary Biology 2019 19:156

    Content type: Research article

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  39. Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Ac...

    Authors: Umberto Rosani, Chang-Ming Bai, Lorenzo Maso, Maxwell Shapiro, Miriam Abbadi, Stefania Domeneghetti, Chong-Ming Wang, Laura Cendron, Thomas MacCarthy and Paola Venier

    Citation: BMC Evolutionary Biology 2019 19:149

    Content type: Research article

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  40. Antioxidative enzymes contribute to a parasite’s ability to counteract the host’s intracellular killing mechanisms. The facultative intracellular oyster parasite, Perkinsus marinus, a sister taxon to dinoflagella...

    Authors: Eric J. Schott, Santiago Di Lella, Tsvetan R. Bachvaroff, L. Mario Amzel and Gerardo R. Vasta

    Citation: BMC Evolutionary Biology 2019 19:146

    Content type: Research article

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  41. Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depend...

    Authors: R. Huttener, L. Thorrez, T. in’t Veld, M. Granvik, L. Snoeck, L. Van Lommel and F. Schuit

    Citation: BMC Evolutionary Biology 2019 19:144

    Content type: Research article

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  42. Our laboratory identified ADGRL4/ELTD1, an orphan GPCR belonging to the adhesion GPCR (aGPCR) family, as a novel regulator of angiogenesis and a potential anti-cancer therapeutic target. Little is known about ...

    Authors: David M. Favara, Alison H. Banham and Adrian L. Harris

    Citation: BMC Evolutionary Biology 2019 19:143

    Content type: Research article

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  43. Previously, we have demonstrated that genes involved in ovarian function are highly conserved throughout evolution. In this study, we aimed to document the conservation of genes involved in spermatogenesis fro...

    Authors: Sophie Fouchécourt, Floriane Picolo, Sébastien Elis, Charlotte Lécureuil, Aurore Thélie, Marina Govoroun, Mégane Brégeon, Pascal Papillier, Jean-Jacques Lareyre and Philippe Monget

    Citation: BMC Evolutionary Biology 2019 19:137

    Content type: Research article

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  44. The evolutionary probability (EP) of an allele in a DNA or protein sequence predicts evolutionarily permissible (ePerm; EP ≥ 0.05) and forbidden (eForb; EP < 0.05) variants. EP of an allele represents an indep...

    Authors: Ravi Patel and Sudhir Kumar

    Citation: BMC Evolutionary Biology 2019 19:133

    Content type: Methodology article

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  45. The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. e...

    Authors: Jingqiu Liao, Renato Hohl Orsi, Laura M. Carroll, Jasna Kovac, Hongyu Ou, Hailong Zhang and Martin Wiedmann

    Citation: BMC Evolutionary Biology 2019 19:132

    Content type: Research article

    Published on:

2019 Journal Metrics

  • Citation Impact
    3.058 - 2-year Impact Factor
    3.252 - 5-year Impact Factor
    1.198 - Source Normalized Impact per Paper (SNIP)
    1.531 - SCImago Journal Rank (SJR)

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