Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 22

System / cell line: populations ✕ Assay: phylogenetic ✕ Clear

Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

hiv-1 four simulated population-based maximum bayesian
ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 9 setups

Has reproduction · 87

Italian brown trout populations are genetically differentiated but show strong admixture from stocking practices, especially with the Atlantic lineage.

brown snp subset salmo ddrad-seq admixture newhybrids
Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

PMID 15984912 · PMC1166350 · PLoS biology · 2005 · 8 claims · 6 setups

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Most mtDNA lineages in Taiwanese aboriginal populations are distinct from those in China and the Taiwan Han population, consistent with descent from the island's initial late Pleistocene settlers

indigenous b4a-lineage southeast populations mtdna complete rflp
Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
Melanesian mtDNA complexity.

PMID 17327912 · PMC1803017 · PloS one · 2007 · 8 claims · 5 setups

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Among-group mtDNA variation in Northern Island Melanesia is structured by island, island size, and language affiliation.

populations near mtdna mtdna analysis coalescence
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.

PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups

Has reproduction · 64

Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)

infantum donovani snp populations whole-genome read admixture
Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA.

PMID 16893451 · PMC1569435 · BMC genetics · 2006 · 8 claims · 4 setups

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Mitochondrial DNA shows no significant difference between Indian tribal and caste populations except higher frequency of west Eurasian-specific haplogroups in upper castes, especially in northwest India

pardhan same comparative mtdna y-chromosome y-str
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population
Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

Has reproduction · 51

K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

uniflora whole-genome phylogenomic population
Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

PMID 15916705 · PMC1180443 · BMC microbiology · 2005 · 8 claims · 8 setups

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H. pylori strains from England are genetically distinct from strains obtained from other countries based on virulence gene analysis (cagT, cagE, cagA, vacA, iceA, oipA, babB)

pylori english pcr sequencing fluorescent
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

PMID 18680585 · PMC2529308 · BMC evolutionary biology · 2008 · 8 claims · 7 setups

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R7a1, a recently derived sub-branch of haplogroup R7, is particularly frequent among Munda-speaking tribal groups

mtdnas haplogroup genetic geographic complete hvs-i reduced-median
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

PMID 19797407 · PMC2778335 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 7 setups

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ProSeq3 is a program with a graphic user interface that simplifies preparation and basic population genetic analysis of multigenic DNA polymorphism datasets

software authors sequence polymorphism phylogenetic
Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex.

PMID 35342602 · PMC8928884 · Ecology and evolution · 2022 · 7 claims · 5 setups

Has reproduction · 87

At least five distinct species exist within the E. ruidum species complex

ruidum cox1 cox1 3rad ultraconserved
Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

PMID 10081674 · PMC2627704 · Emerging infectious diseases · 1999 · 8 claims · 5 setups

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SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America

hantavirus-infected aligned phylogenetic archival rt-pcr maximum bootstrap
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

hg16 genomic individuals element computational pcr pcr-based
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population

Experiments

Direct maximum parsimony phylogeny reconstruction from genotype data.

Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

Melanesian mtDNA complexity.

Candidates for Balancing Selection in Leishmania donovani Complex Parasites.

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

Comparative genomics of Helicobacter pylori isolates recovered from ulcer disease patients in England.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

Processing and population genetic analysis of multigenic datasets with ProSeq3 software.

Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex.

Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.