@article{paulson1973predator,
    author = "Paulson, Dennis R.",
    title = "Predator Polymorphism and Apostatic Selection",
    year = "1973",
    journal = "Evolution",
    url = "https://doi.org/10.2307/2406967",
    doi = "10.2307/2406967",
    number = "2",
    pages = "269",
    volume = "27"
}

@misc{paulson1973predator2,
    author = "Paulson, D. R",
    title = "Predator polymorphism and stochastic selection",
    year = "1973",
    howpublished = "Evolution, v. 27, p. 269-277",
    note = "talkorigins\_source = {true}; raw\_reference = {Paulson, D. R., 1973, Predator polymorphism and stochastic selection: Evolution, v. 27, p. 269-277.}"
}

@misc{kimura1977causes1,
    author = "Kimura, M",
    title = "Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism",
    year = "1977",
    howpublished = "Mishima, Japan, National Institute of Genetics, p. 1-28",
    note = "talkorigins\_source = {true}; raw\_reference = {Kimura, M., 1977, Causes of Evolution and Polymorphism at the Molecular Level, in Kimura, M., ed., Molecular Evolution and Polymorphism: Mishima, Japan, National Institute of Genetics, p. 1-28.}"
}

@article{crossref1985the,
    title = "The Neutral Theory of Molecular Evolution, by Motoo Kimura",
    year = "1985",
    journal = "Molecular Biology and Evolution",
    url = "https://doi.org/10.1093/oxfordjournals.molbev.a040364",
    doi = "10.1093/oxfordjournals.molbev.a040364"
}

@article{doi101139g89009,
    author = "Kimura, M.",
    title = "The neutral theory of molecular evolution and the world view of the neutralists.",
    year = "1989",
    journal = "Genome",
    url = "https://www.semanticscholar.org/paper/cf528095a1870d8bbc17a7e8f6bd8cf974cd96ca",
    doi = "10.1139/G89-009",
    is_oa = "true",
    number = "1",
    pages = "24-31",
    semanticscholar_citation_count = "192",
    semanticscholar_id = "cf528095a1870d8bbc17a7e8f6bd8cf974cd96ca",
    volume = "31"
}

@article{doi101266jjg66367,
    author = "Kimura, M.",
    title = "The neutral theory of molecular evolution: a review of recent evidence.",
    year = "1991",
    journal = "Idengaku zasshi",
    url = "https://www.jstage.jst.go.jp/article/jjg/66/4/66\_4\_367/\_pdf",
    doi = "10.1266/JJG.66.367",
    is_oa = "true",
    number = "4",
    pages = "367-386",
    semanticscholar_citation_count = "93",
    semanticscholar_id = "ba9ea4034e1dd9e75fd9cd45d91c838e7be3850c",
    volume = "66"
}

@article{crossref1992the,
    title = "The causes of molecular evolution",
    year = "1992",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.30-2064",
    doi = "10.5860/choice.30-2064",
    number = "04",
    pages = "30-2064-30-2064",
    volume = "30"
}

@misc{gillespie1992the,
    author = "Gillespie, John H",
    title = "The Causes of Molecular Evolution",
    year = "1992",
    abstract = "This work provides a unified theory that addresses the important problem of the origin and maintenance of genetic variation in natural populations. With modern molecular techniques, variation is found in all species, sometimes at astonishingly high levels. Yet the forces that maintain variation within and between species have been difficult subjects of study. Because they act very weakly and operate over vast time scales, scientists must rely on indirect inferences and speculative mathematical models. The author's research in molecular genetics, evolution, and bio-mathematics has enabled him to draw on his work, and present a coherent and valuable view of the field. The book is divided into three parts. The first addresses protein evolution, DNA evolution, and molecular mechanisms, reviewing the experimental observations on genetic variation. The second gives a unified treatment of the mathematical theory of selection in a fluctuating environment. The final section combines the earlier assessments in a treatment of the scientific status of two competing theories for the maintenance of genetic variation.",
    url = "https://doi.org/10.1093/oso/9780195068832.001.0001",
    doi = "10.1093/oso/9780195068832.001.0001"
}

@article{nachman1996the,
    author = "Nachman, Michael W.",
    title = "The Legacy of Motoo Kimura Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers Motoo Kimura Naoyuki Takahata",
    year = "1996",
    journal = "BioScience",
    url = "https://doi.org/10.2307/1312752",
    doi = "10.2307/1312752",
    number = "3",
    pages = "221-222",
    volume = "46"
}

@article{benowitz2000causes,
    author = "Benowitz, S.",
    title = "Causes of Pain Investigated at Molecular Level",
    year = "2000",
    journal = "Journal of the National Cancer Institute",
    url = "https://doi.org/10.1093/jnci/92.11.868",
    doi = "10.1093/jnci/92.11.868",
    number = "11",
    pages = "868-870",
    volume = "92"
}

@article{doi101007bf01659390,
    author = "Kimura, M. and Ohta, T.",
    title = "On the rate of molecular evolution",
    year = "2005",
    journal = "Journal of Molecular Evolution",
    url = "https://www.semanticscholar.org/paper/3afccf44513c0dc8ea68c2743b1784d035abcb1c",
    doi = "10.1007/BF01659390",
    is_oa = "true",
    number = "1",
    pages = "1-17",
    semanticscholar_citation_count = "129",
    semanticscholar_id = "3afccf44513c0dc8ea68c2743b1784d035abcb1c",
    volume = "1"
}

@article{saakian2008dynamics,
    author = "Saakian, David B. and Rozanova, Olga and Akmetzhanov, Andrei",
    title = "Dynamics of the Eigen and the Crow-Kimura models for molecular evolution",
    year = "2008",
    journal = "Physical Review E",
    url = "https://doi.org/10.1103/physreve.78.041908",
    doi = "10.1103/physreve.78.041908",
    number = "4",
    volume = "78"
}

@article{doi101371journalpgen1005681,
    author = "Natarajan, Chandrasekhar and Projecto-Garcia, J. and Moriyama, H. and Weber, R. and Muñoz-Fuentes, Violeta and Green, A. and Kopuchian, Cecilia and Tubaro, P. and Alza, Luis and Bulgarella, M. and Smith, Matthew M. and Wilson, R. and Fago, A. and McCracken, K. and Storz, J. F.",
    title = "Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level",
    year = "2015",
    journal = "PLoS Genetics",
    abstract = "A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.",
    url = "https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1005681\&type=printable",
    doi = "10.1371/journal.pgen.1005681",
    is_oa = "true",
    number = "12",
    pages = "e1005681",
    semanticscholar_citation_count = "115",
    semanticscholar_id = "47aee0ccbab5adb315b8a03f6ca46e6ce262144e",
    volume = "11"
}

@article{doi103389fmicb201600232,
    author = "Diaz, Maureen H and Winchell, J.",
    title = "The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae",
    year = "2016",
    journal = "Frontiers in Microbiology",
    abstract = "Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.",
    url = "https://www.frontiersin.org/articles/10.3389/fmicb.2016.00232/pdf",
    doi = "10.3389/fmicb.2016.00232",
    is_oa = "true",
    semanticscholar_citation_count = "53",
    semanticscholar_id = "060ac80539683b8016a4dd59b5c85f70cd847f73",
    volume = "7"
}

@article{cortez2017the,
    author = "Cortez, Michael H. and Patel, Swati",
    title = "The Effects of Predator Evolution and Genetic Variation on Predator–Prey Population-Level Dynamics",
    year = "2017",
    journal = "Bulletin of Mathematical Biology",
    url = "https://doi.org/10.1007/s11538-017-0297-y",
    doi = "10.1007/s11538-017-0297-y",
    number = "7",
    pages = "1510-1538",
    volume = "79"
}

@article{doi101016jchemosphere2019125203,
    author = "Lu, Xue-Ping and Xu, L. and Meng, Li-Wei and Wang, Luo-Luo and Niu, J. and Wang, Jinjun",
    title = "Divergent molecular evolution in glutathione S-transferase conferring malathion resistance in the oriental fruit fly, Bactrocera dorsalis (Hendel).",
    year = "2020",
    journal = "Chemosphere",
    abstract = "Insect glutathione S-transferases (GSTs) are important in insecticide detoxification and Insect-specific GSTs, Epsilon and Delta, have largely expanded in insects. In this study, we functionally expressed and characterized an epsilon class GST gene (BdGSTe8), predominant in the adult Malpighian tubules of Bactrocera dorsalis. This gene may be associated with malathion resistance based on transcriptional studies of resistant and susceptible strains. RNA interference-mediated knockdown of this gene significantly recovered malathion susceptibility in the adults of a malathion-resistant strain, and overexpression of BdGSTe8 enhanced resistance in transgenic Drosophila. Analysis of BdGSTe8 polymorphism showed that several point mutations may be associated with metabolic resistance to malathion. A cytotoxicity assay in Escherichia coli indicated that both of the recombinant BdGSTe8 proteins may play a functional role in protecting cells from toxicity. The allele of BdGSTe8-B conferred higher levels of malathion detoxification capability. Liquid chromatography and ultra-performance liquid chromatography-tandem mass spectrometry analysis showed that the BdGSTe8-A allele did not metabolize malathion directly. However, the BdGSTe8-B allele was involved in the direct metabolism of malathion, which was caused by a mutation in V128A. Further analysis of the sequence suggests that BdGSTe8 evolved rapidly. It maybe play the role of a backup gene and could become a new gene in the future in order to retain the ability of detoxification of malathion, which was driven by positive selection. These results suggest that divergent molecular evolution in BdGSTe8 has played a role in metabolic resistance to malathion in B. dorsalis.",
    url = "https://www.semanticscholar.org/paper/04261a26b70cac395030ca25b03ed71f49b7fa54",
    doi = "10.1016/j.chemosphere.2019.125203",
    is_oa = "true",
    pages = "125203",
    semanticscholar_citation_count = "34",
    semanticscholar_id = "04261a26b70cac395030ca25b03ed71f49b7fa54",
    volume = "242"
}

@article{doi103389fgene2022991900,
    author = "Xie, Pengfei and Liu, Jia and Lu, R. and Zhang, Yanmei and Sun, Xiaoqin",
    title = "Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza",
    year = "2022",
    journal = "Frontiers in Genetics",
    abstract = "The exploitation of plant disease resistance (R) genes in breeding programs is an effective strategy for coping with pathogens. An understanding of R gene variation is the basis for this strategy. Rice blast disease, caused by the Magnaporthe oryzae fungus, is a destructive disease of rice. The rice blast resistance gene Pi-d2 represents a new class of plant R gene because of its novel extracellular domain. We investigated the nucleotide polymorphism, phylogenetic topology and evolution patterns of the Pi-d2 gene among 67 cultivated and wild rice relatives. The Pi-d2 gene originated early in the basal Poales and has remained as a single gene without expansion. The striking finding is that susceptible Pi-d2 alleles might be derived from a single nucleotide substitution of the resistant alleles after the split of Oryza subspecies. Functional pleiotropy and linkage effects are proposed for the evolution and retention of the disease-susceptible alleles in rice populations. One set of DNA primers was developed from the polymorphic position to detect the functional nucleotide polymorphism for disease resistance of the Pi-d2 gene based on conventional Polymerase Chain Reaction. The nucleotide diversity level varied between different domains of the Pi-d2 gene, which might be related to distinct functions of each domain in the disease defense response. Directional (or purifying) selection appears dominant in the molecular evolution of the Pi-d2 gene and has shaped its conserved variation pattern.",
    url = "https://www.frontiersin.org/articles/10.3389/fgene.2022.991900/pdf",
    doi = "10.3389/fgene.2022.991900",
    is_oa = "true",
    semanticscholar_citation_count = "6",
    semanticscholar_id = "65291e48a635d47bb10c15449e23ebf20c049fc8",
    volume = "13"
}

@article{doi103390plants13172438,
    author = "Zhang, Lin and Zhao, Panpan and Meng, Qingfang and Yan, Hongfei and Liu, Daqun",
    title = "The Migration, Diversity, and Evolution of Puccinia triticina in China",
    year = "2024",
    journal = "Plants",
    abstract = "Wheat leaf rust, caused by Puccinia triticina, is one of the most common fungal diseases of wheat in China and occurs widely in various wheat-growing regions. To clarify the epidemic, spread rules, and population structure of P. triticina among different regions, 217 isolates of P. triticina collected from Hebei, Shandong, Sichuan, and Xinjiang in China were tested by 34 Thatcher near-isogenic lines and 21 pairs of EST-SSR primers. A total of 83 races were identified, and THTT, PHTT, THTS, and PHJT were the most predominant races in the four provinces in 2009. We found enriched virulence and genetic diversity in the four P. triticina populations and a significant correlation between genetic polymorphism and geographic regions. However, no significant correlation was found between virulence phenotypes and molecular genotypes. Moreover, a notable high level of gene flow (Nm = 2.82 > 1) among four P. triticina populations was detected. The genetic relationship among Hebei, Shandong, and Sichuan populations was close, possibly due to the spread of P. triticina from Sichuan to Shandong and then to Hebei. In contrast, the Xinjiang population was relatively independent. Genetic differentiation analysis showed some level of differentiation among or within populations of P. triticina in the four provinces, and the genetic variation within populations (74.97\%) was higher than across populations (25.03\%). Our study provides a basis for a better understanding of the regional migration, epidemic, and population structure of P. triticina in China.",
    url = "https://doi.org/10.3390/plants13172438",
    doi = "10.3390/plants13172438",
    is_oa = "true",
    number = "17",
    pages = "2438",
    semanticscholar_citation_count = "4",
    semanticscholar_id = "eb41a0ba4e3264431db5863f7a4395a0cc75b73d",
    volume = "13"
}

@article{suvorov2025geometric,
    author = "Suvorov, Vladimir and Solé, Ricard and Saakian, David B.",
    title = "Geometric phase in the Crow-Kimura model of molecular evolution on dynamic environments",
    year = "2025",
    journal = "Physical Review E",
    abstract = "When taking place under fluctuating environments, some classical results of evolutionary dynamics in fitness landscapes need to be reconsidered. Under such nonequilibrium conditions, the properties of adaptive evolution might escape from the expectations grounded in equilibrium systems. Here, an important contribution to this nonequilibrium dynamics results from the presence of a geometry (Berry) phase in the Crow-Kimura model of molecular evolution with asymmetric mutations. By considering changes in fitness alone as well as changes in both fitness and mutation, analytical expressions for the Berry phase are derived, showing strong singularities at bulk transition points. Periodically varying parameters are also analyed for the two-dimensional case. The potential implications for evolutionary and prebiotic scenarios are discussed.",
    url = "https://doi.org/10.1103/rv4q-l8cq",
    doi = "10.1103/rv4q-l8cq",
    number = "5",
    volume = "112"
}

@article{doi1014719pst12683,
    author = "Swati, B. and Chinnakaruppan, M. and Niranjana, Pmp and Yogita, M. and Susheel, K. and Vijayanandraj, S.",
    title = "Molecular characterisation and evolutionary analysis of Papaya ringspot virus infecting papaya (Carica papaya L.)",
    year = "2026",
    journal = "Plant Science Today",
    abstract = "Papaya (Carica papaya L.) is a tropical, commercial fruit with high nutritive and medicinal value. Papaya ringspot virus (PRSV) causes destructive disease in papaya and cucurbit cultivation worldwide. The current study analysed the genetic diversity and phylogenetic relationship of 115 PRSV isolates submitted until December 2024 in NCBI, including one complete genome sequences from Palampur, India characterized in this study. The complete genome of a PRSV Palampur isolate collected during March 2020 from foothills of Himalayan region in northern India was characterized. The Palampur isolate (MW030522.1) showed close identity of 90 \% with Bangladesh isolate (MH397222). Species demarcation analysis of nucleotide sequence revealed one major peak ranging between 79–85 \%. The nucleotide diversity of the PRSV genome was 0.13. The 5’ end of the genome containing the P1 gene showed high levels of polymorphism. Phylogenetic analysis showed 4 major groups (G1-G4) and one recombinant isolate (MH444652). The results suggest that the geographic region, rather than hosts, is the probable factor determining the genetic diversity of PRSV isolates. Neutrality tests and dN/dS ratio showed negative values, indicating purifying selection. The current study deepens understanding of PRSV genetic diversity and evolution, which can be used for development of effective management strategies against PRSV.",
    url = "https://www.semanticscholar.org/paper/7eb1748b2ccc802b1987ed8323562700769a16df",
    doi = "10.14719/pst.12683",
    is_oa = "true",
    semanticscholar_id = "7eb1748b2ccc802b1987ed8323562700769a16df"
}

@article{doi103390microorganisms14040761,
    author = "Xia, Qiqi and Liu, Jian and Gui, Yaping and Xia, Luming and Cao, Chuangui and Chen, Bei-Lei and Yu, Xiangqian and Chen, Weifeng and Xu, Feng and Wang, Jian and Zhao, Hongjin",
    title = "Molecular Characteristics and Genetic Diversity of Canine Parvovirus in Shanghai, China, from 2016 to 2025",
    year = "2026",
    journal = "Microorganisms",
    abstract = "Canine parvovirus (CPV) is a major pathogen causing severe gastroenteritis in dogs. Since its emergence, CPV has undergone continuous evolution, leading to the predominance of variants such as CPV-2a, CPV-2b, and CPV-2c. To characterize the genetic features and evolutionary trends of CPV-2 at a regional level, 775 fecal samples were collected from domestic and stray dogs with suspected CPV-2 infection in Shanghai between 2016 and 2025. The overall positivity rate was 23.2\% (180/775); incidence was substantially higher in stray dogs (30.2\%) than in domestic dogs (15.9\%). Thirty-one CPV-2 strains were successfully isolated. Temporal analysis revealed a pronounced genotype shift: isolates from 2016 to 2020 were predominantly New CPV-2a, whereas CPV-2c became the dominant genotype from 2021 through 2025. Sequence analysis identified the polymorphism of VP2 gene and characteristic mutations F267Y, Y324I, N426E, Q370R and A440T in CPV-2c strains. A novel I447M mutation was detected in several isolates. Phylogenetic analysis showed that Shanghai isolates formed distinct clusters; CPV-2c strains were closely related to the Asian lineage. Structural modeling indicated that mutations at residues L87M, T101I, Y267F, A297S, G300A, Y305D, I324Y, Q370R, N426E, A440T, and I447M may alter the tertiary structure of the VP2 protein, potentially affecting antigenicity and receptor recognition. Collectively, these results demonstrate the complete genotype replacement of CPV-2 in Shanghai; CPV-2c is now predominant. Identification of the novel I447M mutation and structural analysis of key amino acid substitutions provide insight into CPV molecular evolution. These findings suggest that vaccines primarily based on older CPV-2 or CPV-2b genotypes offer suboptimal protection, highlighting the need for updated vaccine strategies targeting prevalent CPV-2c variants.",
    url = "https://www.semanticscholar.org/paper/c5f5af84db0784387494c86465904df2ccd3d21b",
    doi = "10.3390/microorganisms14040761",
    is_oa = "true",
    number = "4",
    pages = "761",
    semanticscholar_id = "c5f5af84db0784387494c86465904df2ccd3d21b",
    volume = "14"
}