Articles

1. Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution

   • Masaya Morita
   • Nozomi Hanahara
   • Ariyo Imanuel Tarigan

   Original Article 25 April 2024

   

2. A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology

   • Rama S. Singh

   Original Article 25 April 2024

3. On Protein Loops, Prior Molecular States and Common Ancestors of Life

   • Kelsey Caetano-Anollés
   • M. Fayez Aziz
   • Gustavo Caetano-Anollés

   Review Open access 23 April 2024

   

4. Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads

   • Leo Douglas Creasey
   • Eran Tauber

   Original Article Open access 18 April 2024

   

5. Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca)

   • Zhenxin Fan
   • Rusong Zhang
   • Jing Li

   Original Article 18 April 2024

   

6. Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation

   • Michael A. Sennett
   • Douglas L. Theobald

   Original Article Open access 19 March 2024 Pages: 181 - 206

   

7. Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host

   • Zaki Saati-Santamaría
   • José David Flores-Félix
   • Eustoquio Martínez-Molina

   Original Article Open access 19 March 2024 Pages: 169 - 180

   

8. GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences

   • Riccardo G. Kyriacou
   • Peter O. Mulhair
   • Peter W. H. Holland

   Original Article Open access 15 March 2024 Pages: 138 - 152

   

9. Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution

   • Manisha Ray
   • Shivakumara Manu
   • Govindhaswamy Umapathy

   Original Article 15 March 2024 Pages: 121 - 137

   

10. Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions

    • Zachery W. Dickson
    • G. Brian Golding

    Original Article 14 March 2024 Pages: 153 - 168

    

11. Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation

    • Michael Schmutzer
    • Pouria Dasmeh
    • Andreas Wagner

    Original Article Open access 12 March 2024 Pages: 104 - 120

    

12. Assembly Theory: What It Does and What It Does Not Do

    • Johannes Jaeger

    Commentary Open access 07 March 2024 Pages: 87 - 92

    

13. Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes

    • Katherine D. Chau
    • Frances E. Hauser
    • Nathan R. Lovejoy

    Original Article 28 February 2024 Pages: 93 - 103

    

14. Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin

    • Benjamin M. Scott
    • Steven K. Chen
    • Belinda S. W. Chang

    Original Article 07 February 2024 Pages: 61 - 71

    

15. FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus

    • Michel Mickael
    • Marzena Łazarczyk
    • Piotr Religa

    Original Article 29 January 2024 Pages: 72 - 86

    

16. Evolution of the Major Components of Innate Immunity in Animals

    • Rafael Cardoso Maciel Costa Silva
    • Fábio Mendonça Gomes

    Review 28 January 2024 Pages: 3 - 20

    

17. Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies

    • Hui Yu
    • Xiaojue Nong
    • Wanzhen Liu

    Original Article 27 January 2024 Pages: 42 - 60

    

18. 2023 Zuckerkandl Prize

    • Caroline M. Weisman
    • Bui Quang Minh
    • David A. Liberles

    Announcement 17 January 2024 Pages: 1 - 2

19. Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1

    • Forrest Weghorst
    • Martí Torres Marcén
    • Karina S. Cramer

    Original Article Open access 08 January 2024 Pages: 30 - 41

    

20. Functional Divergence and Origin of the Vertebrate Praja Family

    • Wataru Onodera
    • Kotaro Kawasaki
    • Toru Asahi

    Original Article 29 December 2023 Pages: 21 - 29

    

21. APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families

    • Cristian E. Cadena-Caballero
    • Nestor Munive-Argüelles
    • Francisco Martinez-Perez

    Original Article Open access 16 December 2023 Pages: 882 - 896

    

22. Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)

    • Gunnar S. Nystrom
    • Schyler A. Ellsworth
    • Darin R. Rokyta

    Original Article 13 December 2023 Pages: 935 - 962

    

23. Origins and Functional Significance of Eukaryotic Protein Folds

    • Martin Romei
    • Mathilde Carpentier
    • Guillaume Lecointre

    Original Article 07 December 2023 Pages: 854 - 864

    

24. The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species

    • Nicholas C. Palmateer
    • James B. Munro
    • Joana C. Silva

    Original Article Open access 28 November 2023 Pages: 897 - 911

    

25. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events

    • Md Lifat Rahi
    • Peter B. Mather
    • David A. Hurwood

    Original Article 27 November 2023 Pages: 976 - 989

    

26. Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians

    • Elisa Ramos
    • Giovanna Selleghin-Veiga
    • Mariana F. Nery

    Original Article 27 November 2023 Pages: 865 - 881

    

27. Unusual Evolution of Cephalopod Tryptophan Indole-Lyases

    • Hajime Julie Yuasa

    Original Article 26 November 2023 Pages: 912 - 921

    

28. Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair

    • Lasha Bukhnikashvili

    Original Article 25 November 2023 Pages: 963 - 975

    

29. Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System

    • Meiming Cai
    • Shuanglin Li
    • Bofeng Zhu

    Original Article 25 November 2023 Pages: 922 - 934

    

30. Functional Diversification and the Plant Secondary Cell Wall

    • Joseph B. Colbert
    • Heather D. Coleman

    Review 18 November 2023 Pages: 761 - 772

31. Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production

    • Alexander Fedosov
    • Carmen Federica Tucci
    • Nicolas Puillandre

    Original Article Open access 14 November 2023 Pages: 837 - 853

    

32. Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors

    • Abigail García-Morales
    • Daniel Balleza

    Original Article 13 November 2023 Pages: 819 - 836

    

33. Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins

    • Sitara Palecanda
    • Elizabeth Madrid
    • Megan L. Porter

    Original Article 09 November 2023 Pages: 806 - 818

    

34. Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress

    • Wei Chi
    • Juanjuan Fu
    • Libin Zhou

    Original Article 04 November 2023 Pages: 780 - 792

    

35. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species

    • Johnny Sousa Ferreira
    • Daniel Pacheco Bruschi

    Original Article 31 October 2023 Pages: 793 - 805

    

36. The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees

    • Alberto Fernández
    • Natàlia Segura-Alabart
    • Francesc Serratosa

    Original Article Open access 21 October 2023 Pages: 773 - 779

    

37. Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network

    • Hayley Boigenzahn
    • Leonardo D. González
    • John Yin

    Original Article 05 October 2023 Pages: 730 - 744

    

38. Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius

    • Kyomi Nagasawa
    • Takashi Kitano

    OriginalPaper 03 October 2023 Pages: 745 - 760

    

39. Left–Right Reversal Recurrently Evolved Regardless of Diaphanous-Related Formin Gene Duplication or Loss in Snails

    • Takeshi Noda
    • Noriyuki Satoh
    • Takahiro Asami

    Original Article Open access 25 September 2023 Pages: 721 - 729

    

40. A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine

    • Rama S. Singh

    Original Article Open access 04 September 2023 Pages: 711 - 720

    

41. Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection

    • Michael A. Savageau

    Original Article Open access 25 August 2023 Pages: 687 - 710

    

42. Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery

    • Pavan Gollapalli
    • Sushmitha Rudrappa
    • Hulikal Shivashankara Santosh Kumar

    Review 25 August 2023 Pages: 598 - 615

    

43. Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei

    • Motofumi Saito
    • Rerina Inose
    • Akio Kanai

    Original Article Open access 22 August 2023 Pages: 669 - 686

    

44. Pangenomic Analysis of Nucleo-Cytoplasmic Large DNA Viruses. I: The Phylogenetic Distribution of Conserved Oxygen-Dependent Enzymes Reveals a Capture-Gene Process

    • J. A. Campillo-Balderas
    • A. Lazcano
    • A. Becerra

    Original Article Open access 01 August 2023 Pages: 647 - 668

    

45. Informatic Capabilities of Translation and Its Implications for the Origins of Life

    • Bruno Cuevas-Zuviría
    • Zachary R. Adam
    • Betül Kaçar

    Random Walking 01 August 2023 Pages: 567 - 569

46. Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes

    • Diksha Bhalla
    • Vera van Noort

    Original Article 01 July 2023 Pages: 628 - 646

    

47. Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants

    • Natalia Żyła
    • Danuta Babula-Skowrońska

    Review Open access 23 June 2023 Pages: 581 - 597

    

48. A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila

    • Soumen Khan
    • Saurabh J. Pradhan
    • L. S. Shashidhara

    Original Article 21 June 2023 Pages: 616 - 627

    

49. Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty

    • Zachary Ardern

    Mini-Review 16 June 2023 Pages: 570 - 580

    

50. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium

    • Ramses Alejandro Rosales-García
    • Rhett M. Rautsaw
    • Christopher L. Parkinson

    Original Article 03 June 2023 Pages: 514 - 535