Topic 40

evolutionary phylogenetic evolution species genomes lineages history genome phylogeny tree genomic ancestral origin ancient diversity divergence clade genus diversification biology sequences analyses ancestor lineage clades gene sequence among family taxa diverse relationships genes all group genomics duplication extant evolved phylogenomic families trees genetic ago years evidence closely comparative three groups speciation some origins events other conserved eukaryotes common diverged most recent taxonomic distribution across morphological genera geographic hybridization last divergent sister inferred south originated conservation inference occurred horizontal two million vertebrates patterns life have plant major ancestors within from ecological africa reconstruction members related sequenced modern fossil elements ancestry likely

815 items. Top items listed below.

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods 81 40 31 21 9 5

Bats are key hosts in the radiation of mammal-associated Bartonella bacteria 40 5

A New Tree-Based Methodological Framework to Infer the Evolutionary History of Mesopolyploid Lineages: An Application to the Brassiceae Tribe (Brassicaceae). 40 4

Phenotypic reconstruction of the last universal common ancestor reveals a complex cell 40 21 5 4

Intragenic conflict in phylogenomic datasets 40 21 4

P-elements strengthen reproductive isolation within the Drosophila simulans species complex 81 21 5

Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe) 40 21 5

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny 40 5

Color polymorphism is a driver of diversification in the lizard family Lacertidae 40 21 5

Evolutionary patterns of 64 vertebrate genomes (species) revealed by phylogenomics analysis of protein-coding gene families 40 5 4

Abundantly expressed class of non-coding RNAs conserved through the multicellular evolution of dictyostelid social amoebae 40 9 5

Molecular Evolution of the Sex Peptide Network in Drosophila 56 21 5

Animal chromosome counts reveal similar range of chromosome numbers but with less polyploidy in animals compared to flowering plants 40 21 5

Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses 40 5

Characterising the methylome of Legionellalongbeachae serogroup 1 clinical isolates and assessing geo-temporal genetic diversity 121 40 12 5

Panoramic Insights into the Microevolution and Macroevolution of Prevotella copri-containing Lineage in Primate Guts 143 40 29 5

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus 121 40 5

Mitochondrial fostering: the mitochondrial genome may play a role in plant orphan gene evolution 21 16 5 4

Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l. 40 5 4

Evolutionary and Comparative Analysis of bacterial Non-Homologous End Joining Repair 46 40 21 5

Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity 40 21 5

Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes 40 5

Mycena genomes resolve the evolution of fungal bioluminescence 40 5

Factors influencing the accuracy in dating single gene trees 40 21 5 4

Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea). 40 21 5

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

The bear bones: mosaic ancestry of Macaca arctoides explains divergent baculum morphology 40 21 5

Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-Cov-2 37 21 5 1

Phylogenetic diversification of sirtuin genes with a description of a new family member 40 5

When species trees disagree: an approach consistent with the coalescent that quantifies phylogenomic support for contentious relationships 83 40 4

Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana 134 9 5

The legacy of recurrent introgression during the radiation of hares 40 21 5

Evolution of conserved noncoding sequences in Arabidopsis thaliana 134 40 9 5

Long identical sequences found in multiple bacterial genomes reveal frequent and widespread exchange of genetic material between distant species. 40 21 5 4

Genome-Wide Search for Candidate Drivers of Adaptation Reveals Genes Enriched for Shifts in Purifying Selection (SPurS) 21 5 4

Repetitive DNA profiles reveal evidence of rapid genome evolution and reflect species boundaries in ground beetles 40 21 5 4

Reconstructing the history and biological consequences of a plant invasion on the Galapagos islands 21 5

Ecological specialization promotes diversity and diversification in the East Mediterranean genus Ricotia (Brassicaceae) 40 5

Museum genomics illuminate the high specificity of a bioluminescent symbiosis across a genus of reef fish 40 21 5

Frequent branch-specific changes of protein substitution rates in closely related lineages 40 21 5

Sequence of a Coxiella endosymbiont of the tick Amblyomma nuttalli suggests a pattern of convergent genome reduction in the Coxiella genus 40 5

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN 40 4

Experimental evolution confirms signatures of sexual selection in genomic divergence. 21 5

Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation 132 21 5

Transposon- and genome dynamics in the fungal genus Neurospora: insights from nearly gapless genome assemblies 81 40 5

Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize 81 40 9 5

Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes 40 21 4

Novel non-transposable-element regulation patterns of KZFP family reveal new drivers of its rapid evolution 81 40 21 9 5

The landscape of micro-inversions provides clues for population genetic analysis of humans 40 5

Metagenomic association analysis of gut symbiont Lactobacillus reuteri without host-specific genome isolation 121 29 12 5 4

Insights into chloroplast genome variation across Opuntioideae (Cactaceae) 40 5

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach 37 1

Ecological opportunity as a driving force of radiation events and time-dependent evolutionary rates in papillomaviruses 40 21 5

Phylogenetic signal is associated with the degree of variation in root-to-tip distances 83 40 21 5 4

Unveiling Crucivirus Diversity by Mining Metagenomic Data 121 40 5

Ecological specialisation and evolutionary reticulation in extant Hyaenidae 40 21 5

A large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogen Claviceps purpurea 21 5

An introgressed gene causes meiotic drive in Neurospora sitophila 40 21 5

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens 37 1

Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates 40 5

Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees 40 25 5 4

Features of Functional Human Genes. 121 40 9 5 4

Identification of hidden population structure in time-scaled phylogenies 83 40 21 5 4

Universal and taxon-specific trends in protein sequences as a function of age 40 21 5

Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences 40 5

Focusing on human haplotype diversity in numerous individual genomes demonstrates an evolutional feature of each locus 40 21 5 4

Mitogenomic Phylogeny of Callithrix with Special Focus on Human Transferred Taxa 40 5

Epistasis and physico-chemical constraints contribute to spatial clustering of amino acid substitutions in protein evolution. 21 5

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae) 40 21 5 4

Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae 40 5

Expanding magnetic organelle biogenesis in the domain Bacteria 40 5


Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations 21 5 4

Phylogenomic Insights into the Origin of Primary Plastids 40 5

Revisiting the Genomic Structure of the Genus Pseudomonas with Whole Genome Data: Insights into Diversity and Host-related Genetic Determinants 121 114 12 5

Rooting morphologically divergent taxa - slow-evolving sequence data might help 40 5

Nucleotide substitutions during speciation may explain substitution rate variation 83 40 21 5

Species Tree Inference under the Multispecies Coalescent on Data with Paralogs is Accurate 83 40 21 4

Evolution of regulatory networks associated with traits under selection in cichlids 134 21 9 5

Genome Wide Analysis of Dinucleotide Distribution along the Genomes of Species and its Biological Implication 40 5

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 40 25 4

Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks 21 5

The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases 40 5

Unravelling the evolutionary relationships of hepaciviruses within and across rodent hosts 40 5

From scales to armour: scale losses and trunk bony plate gains in ray-finned fishes 40 5

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae) 40 5 4

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus 1

Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs 40 21 5

Evolution and Ecology in Widespread Acoustic Signaling Behavior Across Fishes 40 5

Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History and Discovery of Novel Players 40 21 5

The timing of human adaptation from Neanderthal introgression 21 5

Evolution at two time-frames: ancient and common origin of two structural variants involved in local adaptation of the European plaice (Pleuronectes platessa) 21 5

The complex evolution of the HSP70 gene family 40 21 5

The evolution of sex-biased gene expression in the Drosophila brain 56 21 9 5

Heliconius butterflies host characteristic and phylogenetically structured adult-stage microbiomes 143 29 5

Population analysis of Legionella pneumophila reveals the basis of resistance to complement-mediated killing 121 114 12 5

Balancing selection maintains ancient genetic diversity in C. elegans 21 5

Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses 37 5

Evolution of a sex megachromosome 40 21 5