Neutral theory of molecular evolution
View article: Adaptive and nonadaptive sequence evolution in short introns of fruit flies of the genus Drosophila
Adaptive and nonadaptive sequence evolution in short introns of fruit flies of the genus Drosophila Open
A major objective in evolutionary biology is to understand the evolutionary processes driving molecular evolution. Earlier, population genetics sought to understand these processes by theoretical insights, leading to heated debates over co…
View article: Model of Three Species Commensalism-Amensalism Symbiosis with Beddington-DeAngelis Functional Responses
Model of Three Species Commensalism-Amensalism Symbiosis with Beddington-DeAngelis Functional Responses Open
This study investigates the dynamical behavior of a three species ecological system involving unilateral interactions of commensalism and amensalism with Beddington–DeAngelis functional responses. The positivity, boundedness, existence, an…
View article: Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations
Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations Open
This deposit contains the data and scripts associated with the manuscript, "Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations." This work addresses a fundamenta…
View article: Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations
Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations Open
This deposit contains the data and scripts associated with the manuscript, "Landscape-scale patterns of beta-diversity in Amazonian canopy trees reveals environmental filtering beyond neutral expectations." This work addresses a fundamenta…
View article: Neutral rate of interest in a small open economy: The case of Canada
Neutral rate of interest in a small open economy: The case of Canada Open
The neutral rate of interest is an important concept and communication tool for central banks. We develop a structural macroeconomic model to study the determinants of the neutral real rate of interest in a small open economy. The model ca…
View article: The phylogenetic Janzen-Connell effect can explain multiple macroecological and macroevolutionary patterns
The phylogenetic Janzen-Connell effect can explain multiple macroecological and macroevolutionary patterns Open
The classical Janzen-Connell (J-C) hypothesis states that species-specific natural enemies induce local-density dependence which explains high diversity observed in tropical tree communities. Recent studies have extended the hypothesis to …
View article: Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes
Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes Open
This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecolo…
View article: Experimental Immigration Mediates Ecological Selection and Drift in Monarch Microbiome Assembly
Experimental Immigration Mediates Ecological Selection and Drift in Monarch Microbiome Assembly Open
The distribution of biodiversity depends on processes operating across scales, yet multiscale paradigms have struggled to permeate host‐microbiome research. Instead, host‐microbiome research has focused on host selection and has struggled …
View article: Phylogenomic Analyses and <scp>DNA</scp> Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution
Phylogenomic Analyses and <span>DNA</span> Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution Open
Moraceae, with its seven tribes, 45 genera, and approximately 1200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogen…
View article: Table 1_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 1_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 6_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 6_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 4_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xls
Table 4_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xls Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 8_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 8_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 2_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 2_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 5_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 5_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 3_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 3_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Table 7_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx
Table 7_Comparative chloroplast genomics of Rutaceae: structural divergence, adaptive evolution, and phylogenomic implications.xlsx Open
The study of chloroplast genome evolutionary dynamics provides critical insights into plant adaptive evolution and phylogenetic relationships. This research conducted a systematic comparative analysis of chloroplast genomes across 35 speci…
View article: Description for S3 Fig.
Description for S3 Fig. Open
Species occupy diverse, heterogeneous environments, which expose populations to spatially varied selective pressures. Populations in different environments can diverge due to local adaptation. However, neutral evolution can also drive pop…
View article: Explanations for S1 Fig.
Explanations for S1 Fig. Open
Species occupy diverse, heterogeneous environments, which expose populations to spatially varied selective pressures. Populations in different environments can diverge due to local adaptation. However, neutral evolution can also drive pop…
View article: Model of a sweep with two meiotic events.
Model of a sweep with two meiotic events. Open
An important aim of population genetics is to elucidate the processes affecting genetic diversity across regions of the genome and across species. Canonical population genetic models of sexually reproducing species define the rate of meio…
View article: Beyond recombination: Exploring the impact of meiotic frequency on genome-wide genetic diversity
Beyond recombination: Exploring the impact of meiotic frequency on genome-wide genetic diversity Open
An important aim of population genetics is to elucidate the processes affecting genetic diversity across regions of the genome and across species. Canonical population genetic models of sexually reproducing species define the rate of meiot…
View article: Neutral genetic diversity during selective sweeps in nonrecombining populations
Neutral genetic diversity during selective sweeps in nonrecombining populations Open
Selective sweeps, resulting from the spread of beneficial, neutral, or deleterious mutations through a population, shape patterns of genetic variation at linked neutral sites. While many theoretical, computational, and statistical advances…
View article: The dominant–egalitarian transition in species-rich communities
The dominant–egalitarian transition in species-rich communities Open
Diverse communities of competing species are generally characterized by substantial niche overlap and strongly stochastic dynamics. Abundance fluctuations are proportional to population size, so the dynamics of rare populations is slower. …
View article: Neutral Theory, Stochasticity, and the Efficiency of Social Institutions
Neutral Theory, Stochasticity, and the Efficiency of Social Institutions Open
This paper draws on the concept of neutral theory from molecular biology to describe how rational choice foundations may be given to cultural practices or social institutions such that the specifics of the practice or institution are inher…
View article: Temporal beta‐diversity patterns are highly dependent on fundamental parameters of neutral dynamics
Temporal beta‐diversity patterns are highly dependent on fundamental parameters of neutral dynamics Open
Temporal changes in community composition, known as temporal beta diversity, are a facet of biodiversity change. Macroecological patterns of temporal beta diversity have gained attention due to the recent biodiversity crisis. However, litt…
View article: Genetic diversity metrics and neutrality tests of <i>H. contortus</i> populations in Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for <i>H. contortus</i> populations from various farms in Scotland and England, highlighting key differences between the two regions. The genetic diversity metrics include the number of sequences, number of ASVs, sequences per ASV, ASV diversity (Hd), the number of segregation sites (S), the number of mutations (Eta), and nucleotide diversity (π). The neutrality tests include Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* statistics, along with their respective significance levels (SigD, SigD*, and SigF*). Statistical significance is denoted by ‘#’ for P < 0.10, ‘*’ for P < 0.05, ‘**’ for P < 0.01, and ‘***’ for P < 0.001. Additionally, ‘n.s.’ indicates results not statistically significant, and ‘n.d.’ denotes data not determined.
Genetic diversity metrics and neutrality tests of <i>H. contortus</i> populations in Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for <i>H. contortus</i> populations from various farms in Scotland and England, highlighting key differences between the two regions. The genetic diversity metrics include the number of sequences, number of ASVs, sequences per ASV, ASV diversity (Hd), the number of segregation sites (S), the number of mutations (Eta), and nucleotide diversity (π). The neutrality tests include Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* statistics, along with their respective significance levels (SigD, SigD*, and SigF*). Statistical significance is denoted by ‘#’ for P < 0.10, ‘*’ for P < 0.05, ‘**’ for P < 0.01, and ‘***’ for P < 0.001. Additionally, ‘n.s.’ indicates results not statistically significant, and ‘n.d.’ denotes data not determined. Open
Genetic diversity metrics and neutrality tests of H. contortus populations in Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for H. contortus populations from various…
View article: Genetic diversity metrics and neutrality tests of <i>T. circumcincta</i> populations from Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for <i>T. circumcincta</i> populations from various farms in Scotland and England, highlighting key differences between the two regions. The genetic diversity metrics include the number of sequences, number of ASVs, sequences per ASV, ASV diversity (Hd), the number of segregation sites (S), the number of mutations (Eta), and nucleotide diversity (π). The neutrality tests include Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* statistics, along with their respective significance levels (SigD, SigD*, and SigF*). Statistical significance is denoted by ‘#’ for P < 0.10, ‘*’ for P < 0.05, ‘**’ for P < 0.01, and ‘***’ for P < 0.001. Additionally, ‘n.s.’ indicates results not statistically significant, and ‘n.d.’ denotes not determined.
Genetic diversity metrics and neutrality tests of <i>T. circumcincta</i> populations from Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for <i>T. circumcincta</i> populations from various farms in Scotland and England, highlighting key differences between the two regions. The genetic diversity metrics include the number of sequences, number of ASVs, sequences per ASV, ASV diversity (Hd), the number of segregation sites (S), the number of mutations (Eta), and nucleotide diversity (π). The neutrality tests include Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* statistics, along with their respective significance levels (SigD, SigD*, and SigF*). Statistical significance is denoted by ‘#’ for P < 0.10, ‘*’ for P < 0.05, ‘**’ for P < 0.01, and ‘***’ for P < 0.001. Additionally, ‘n.s.’ indicates results not statistically significant, and ‘n.d.’ denotes not determined. Open
Genetic diversity metrics and neutrality tests of T. circumcincta populations from Scottish and English farms. This table presents the genetic diversity metrics and neutrality test results for T. circumcincta populations from…
View article: The Constructive Neutral Evolution of Behaviour
The Constructive Neutral Evolution of Behaviour Open
There is an unrecognised disagreement between those studying molecular evolution and those studying behavioural evolution. Only natural selection is ordinarily thought to systematically increase behavioural complexity, but molecular biolog…
View article: Darwin’s Abominable Mystery: DNA Replication Timing, Genome Stability and Biodiversity
Darwin’s Abominable Mystery: DNA Replication Timing, Genome Stability and Biodiversity Open
Both adaptive and non-adaptive theories of evolution have been proposed to explain the process of speciation: how natural selection operates on individuals and populations. Non-adaptive theories emphasize the force of genetic drift in driv…
View article: Table 1_Genetic and codon usage analyses reveal the evolution of the seoul virus.docx
Table 1_Genetic and codon usage analyses reveal the evolution of the seoul virus.docx Open
Introduction Seoul virus (Orthohantavirus seoulense, SEOV), a member of the Hantaviridae, causes hemorrhagic fever with renal syndrome (HFRS) through rodent hosts. However, its molecular evolutionary dynamics and codon usage patterns remai…