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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. Approximately 1000 protein encoding genes common for vertebrates are still unannotated in avian genomes. Are these genes evolutionary lost or are they not yet found for technical reasons? Using genome landscap...

    Authors: R. Huttener, L. Thorrez, T. In’t Veld, M. Granvik, L. Van Lommel, E. Waelkens, R. Derua, K. Lemaire, L. Goyvaerts, S. De Coster, J. Buyse and F. Schuit
    Citation: BMC Ecology and Evolution 2021 21:176
  2. Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we me...

    Authors: Raf Huttener, Lieven Thorrez, Thomas in‘t Veld, Barney Potter, Guy Baele, Mikaela Granvik, Leentje Van Lommel and Frans Schuit
    Citation: BMC Ecology and Evolution 2021 21:153
  3. hes genes are chordate homologs of Drosophila genes, hairy and enhancer of split, which encode a basic helix-loop-helix (bHLH) transcriptional repressor with a WRPW motif. Various developmental functions of hes g...

    Authors: Aya Kuretani, Takayoshi Yamamoto, Masanori Taira and Tatsuo Michiue
    Citation: BMC Ecology and Evolution 2021 21:147
  4. 18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core struct...

    Authors: Olaf R. P. Bininda-Emonds
    Citation: BMC Ecology and Evolution 2021 21:118

    The Correction to this article has been published in BMC Ecology and Evolution 2023 23:23

  5. The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into ...

    Authors: Xiu-Lian Cai, Jacob B. Landis, Hong-Xin Wang, Jian-Hua Wang, Zhi-Xin Zhu and Hua-Feng Wang
    Citation: BMC Ecology and Evolution 2021 21:103
  6. Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs...

    Authors: Ivalú M. Ávila Herrera, Jiří Král, Markéta Pastuchová, Martin Forman, Jana Musilová, Tereza Kořínková, František Šťáhlavský, Magda Zrzavá, Petr Nguyen, Pavel Just, Charles R. Haddad, Matyáš Hiřman, Martina Koubová, David Sadílek and Bernhard A. Huber
    Citation: BMC Ecology and Evolution 2021 21:75

    The Correction to this article has been published in BMC Ecology and Evolution 2021 21:93

  7. Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevice...

    Authors: Fan Li, Yunyun Lv, Zhengyong Wen, Chao Bian, Xinhui Zhang, Shengtao Guo, Qiong Shi and Daiqin Li
    Citation: BMC Ecology and Evolution 2021 21:72
  8. Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human bein...

    Authors: Jiao Peng, Yunlin Zhao, Meng Dong, Shiquan Liu, Zhiyuan Hu, Xiaofen Zhong and Zhenggang Xu
    Citation: BMC Ecology and Evolution 2021 21:71
  9. Color vision and phototactic behavior based on opsins are important for the fitness of insects because of their roles in foraging and mate choice. Related topics, including the duplication and loss of opsin ge...

    Authors: Pengjun Xu, Bin Lu, Jiangtao Chao, Robert Holdbrook, Gemei Liang and Yanhui Lu
    Citation: BMC Ecology and Evolution 2021 21:66
  10. The Type I interferon response is an important first-line defense against viruses. In turn, viruses antagonize (i.e., degrade, mis-localize, etc.) many proteins in interferon pathways. Thus, hosts and viruses ...

    Authors: Elena N. Judd, Alison R. Gilchrist, Nicholas R. Meyerson and Sara L. Sawyer
    Citation: BMC Ecology and Evolution 2021 21:65
  11. Pathogens are key components in natural and agricultural plant systems. There is evidence of evolutionary changes in disease susceptibility as a consequence of climate change, but we know little about the unde...

    Authors: Niamh B. O’Hara, Steven J. Franks, Nolan C. Kane, Silas Tittes and Joshua S. Rest
    Citation: BMC Ecology and Evolution 2021 21:61
  12. The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively...

    Authors: Solène Brohard-Julien, Vincent Frouin, Vincent Meyer, Smahane Chalabi, Jean-François Deleuze, Edith Le Floch and Christophe Battail
    Citation: BMC Ecology and Evolution 2021 21:59
  13. Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant archit...

    Authors: Man Zhang, Ping Li, Xiaolan Yan, Jia Wang, Tangren Cheng and Qixiang Zhang
    Citation: BMC Ecology and Evolution 2021 21:32
  14. Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and ...

    Authors: Jifeng Zhang, Guopen Miao, Shunjie Hu, Qi Sun, Hengwu Ding, Zhicheng Ji, Pen Guo, Shoubao Yan, Chengrun Wang, Xianzhao Kan and Liuwang Nie
    Citation: BMC Ecology and Evolution 2021 21:19
  15. The domestication of tree shrews represents an important advance in the development of standardized laboratory animals. Little is known regarding the miRNA changes that accompany the transformation of wild tre...

    Authors: Caixia Lu, Mingxue Li, Xiaomei Sun, Na Li, Wenguang Wang, Pinfen Tong and Jiejie Dai
    Citation: BMC Ecology and Evolution 2021 21:12
  16. The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. ston...

    Authors: Nathalie Le Roy, Philippe Ganot, Manuel Aranda, Denis Allemand and Sylvie Tambutté
    Citation: BMC Ecology and Evolution 2021 21:1
  17. Eukaryotic protein-coding genes consist of exons and introns. Exon–intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the ra...

    Authors: Irina V. Poverennaya, Nadezhda A. Potapova and Sergey A. Spirin
    Citation: BMC Evolutionary Biology 2020 20:164
  18. K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome...

    Authors: Zhenhua Yang, Hong Li, Yun Jia, Yan Zheng, Hu Meng, Tonglaga Bao, Xiaolong Li and Liaofu Luo
    Citation: BMC Evolutionary Biology 2020 20:157
  19. Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main are...

    Authors: Perla Farhat, Sonja Siljak-Yakovlev, Nicolas Valentin, Carlos Fabregat, Silvia Lopez-Udias, Carlos Salazar-Mendias, Joaquín Altarejos and Robert P. Adams
    Citation: BMC Evolutionary Biology 2020 20:148
  20. Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests s...

    Authors: Yu-Chi Chen, Hao-Chih Kuo, Wen-Sui Lo and Chih-Ming Hung
    Citation: BMC Evolutionary Biology 2020 20:147
  21. On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin o...

    Authors: Zhi-xin Chai, Jin-wei Xin, Cheng-fu Zhang, Dawayangla, Luosang, Qiang Zhang, Pingcuozhandui, Chao Li, Yong Zhu, Han-wen Cao, Hui Wang, Jian-lin Han, Qiu-mei Ji and Jin-cheng Zhong
    Citation: BMC Evolutionary Biology 2020 20:137
  22. Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, incl...

    Authors: Miguel Araujo-Voces and Víctor Quesada
    Citation: BMC Evolutionary Biology 2020 20:135
  23. Two gerbil species, sand rat (Psammomys obesus) and Mongolian jird (Meriones unguiculatus), can become obese and show signs of metabolic dysregulation when maintained on standard laboratory diets. The genetic bas...

    Authors: Yichen Dai, Rodrigo Pracana and Peter W. H. Holland
    Citation: BMC Evolutionary Biology 2020 20:134
  24. 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

    The Correction to this article has been published in BMC Evolutionary Biology 2020 20:132

  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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

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