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Sympatric and allopatric differentiation delineates population structure in free-living terrestrial bacteria

https://doi.org/10.1101/644468
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Outgoing claims: the papers this work cites, builds on, or argues with.

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A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations
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Horizontal gene transfer and the evolution of bacterial and archaeal population structure
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Ordering microbial diversity into ecologically and genetically cohesive units
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The ecology of transfer of mobile genetic elements
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Quantitative and qualitative microscale distribution of bacteria in soil
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A comparison of homologous recombination rates in bacteria and archaea
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Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils
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A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse
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Explaining microbial genomic diversity in light of evolutionary ecology
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Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa
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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
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Genomics, environmental genomics and the issue of microbial species
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Microbial diversity and soil functions
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The importance of resolving biogeographic patterns of microbial microdiversity
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Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations
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Bacterial Species and Speciation
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Roary: rapid large-scale prokaryote pan genome analysis
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ISOLATION BY DISTANCE
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Recombination Shapes the Natural Population Structure of the Hyperthermophilic Archaeon Sulfolobus islandicus
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PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R
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Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus
inferredcites →https://doi.org/10.1093/molbev/msy078openalex-snapshot
Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics
inferredcites →https://doi.org/10.1093/nar/gkj014openalex-snapshot
ISfinder: the reference centre for bacterial insertion sequences
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gkr846openalex-snapshot
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
inferredcites →https://doi.org/10.1093/nar/gks406openalex-snapshot
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
inferredcites →https://doi.org/10.1093/nar/gkw569openalex-snapshot
NCBI prokaryotic genome annotation pipeline
inferredcites →https://doi.org/10.1093/nar/gky425openalex-snapshot
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
inferredcites →https://doi.org/10.1111/1462-2920.13420openalex-snapshot
Latitude delineates patterns of biogeography in terrestrial Streptomyces
inferredcites →https://doi.org/10.1111/1462-2920.14405openalex-snapshot
Emergence of soil bacterial ecotypes along a climate gradient
inferredcites →https://doi.org/10.1111/2041-210x.12382openalex-snapshot
LEA: An R package for landscape and ecological association studies
inferredcites →https://doi.org/10.1111/ejss.4_12398openalex-snapshot
Microbial diversity and soil functions
inferredcites →https://doi.org/10.1111/evo.12258openalex-snapshot
GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?
inferredcites →https://doi.org/10.1111/j.1462-2920.2007.01440.xopenalex-snapshot
Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes
inferredcites →https://doi.org/10.1111/mec.12938openalex-snapshot
Isolation by environment
inferredcites →https://doi.org/10.1111/mec.13132openalex-snapshot
Genetic isolation between two recently diverged populations of a symbiotic fungus
inferredcites →https://doi.org/10.1126/science.1086909openalex-snapshot
Geographic Barriers Isolate Endemic Populations of Hyperthermophilic Archaea
inferredcites →https://doi.org/10.1126/science.1118052openalex-snapshot
Niche Partitioning Among Prochlorococcus Ecotypes Along Ocean-Scale Environmental Gradients
inferredcites →https://doi.org/10.1126/science.1127573openalex-snapshot
Recombination and the Nature of Bacterial Speciation
inferredcites →https://doi.org/10.1126/science.1155532openalex-snapshot
Convergence of Campylobacter Species: Implications for Bacterial Evolution
inferredcites →https://doi.org/10.1126/science.1157890openalex-snapshot
Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton
inferredcites →https://doi.org/10.1126/science.1218198openalex-snapshot
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
inferredcites →https://doi.org/10.1126/science.1248575openalex-snapshot
Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus
inferredcites →https://doi.org/10.1128/mbio.01809-17openalex-snapshot
Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits
inferredcites →https://doi.org/10.1128/mbio.02200-15openalex-snapshot
A Latitudinal Diversity Gradient in Terrestrial Bacteria of the GenusStreptomyces
inferredcites →https://doi.org/10.1128/microbe.9.111.1openalex-snapshot
Bypassing Cultivation To Identify Bacterial Species
inferredcites →https://doi.org/10.12688/f1000research.1-16.v1openalex-snapshot
Is the pan-genome also a pan-selectome?
inferredcites →https://doi.org/10.1371/journal.pbio.1001265openalex-snapshot
Patterns of Gene Flow Define Species of Thermophilic Archaea
inferredcites →https://doi.org/10.1371/journal.pcbi.1004041openalex-snapshot
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
inferredcites →https://doi.org/10.1371/journal.pcbi.1004095openalex-snapshot
Inferring Horizontal Gene Transfer
inferredcites →https://doi.org/10.1371/journal.pgen.1000808openalex-snapshot
The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics
inferredcites →https://doi.org/10.1371/journal.pgen.1005860openalex-snapshot
What Is Speciation?
inferredcites →https://doi.org/10.1371/journal.pone.0011147openalex-snapshot
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
inferredcites →https://doi.org/10.1534/genetics.107.086405openalex-snapshot
Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes
inferredcites →https://doi.org/10.1534/genetics.113.160572openalex-snapshot
Fast and Efficient Estimation of Individual Ancestry Coefficients
inferredcites →https://doi.org/10.3389/fmicb.2016.01874openalex-snapshot
Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

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inferred← citeshttps://doi.org/10.1101/2021.06.30.449460openalex-snapshot
Partners in space: Discordant population structure between legume hosts and rhizobium symbionts in their native range
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