ArticleMolecular biology and evolution2016
Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 87 citations in OpenAlex.
- Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids.Integrative zoology · 2026Article
- CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.Nucleic acids research · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Genomic adaptations for tail-length evolution in arboreal snakes.Molecular biology and evolution · 2026Article
- Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles.Annual review of genetics · 2025Review
- Detecting Convergence of Amino Acid Physicochemical Properties Underlying the Organismal Adaptive Convergent Evolution.Molecular ecology resources · 2025Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Prediction of local convergent shifts in evolutionary rates with phyloConverge.Bioinformatics (Oxford, England) · 2025Article
- Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles.Molecular biology and evolution · 2024Article
- A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution.PLoS computational biology · 2024Article
- PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.Molecular biology and evolution · 2023Article
- Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.Molecular biology and evolution · 2023Article
- Evolutionary constraint and innovation across hundreds of placental mammals.Science (New York, N.Y.) · 2023Article
- Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages.bioRxiv : the preprint server for biology · 2023Article
- Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways.Genetics and molecular biology · 2023Article
- Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness.eLife · 2022Article
- Vision-related convergent gene losses revealeLife · 2022Article
- Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.BMC genomics · 2022Article
- Transcription Factors Evolve Faster Than Their Structural Gene Targets in the Flavonoid Pigment Pathway.Molecular biology and evolution · 2022Article
Corrections and comments
- Commented on by
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3) computing a statistical significance. We demonstrate on large-scale simulated data and on real data that both new methods substantially improve the sensitivity to detect associations between phenotypic and genomic differences. We applied these new methods to detect genomic differences involved in the loss of vision in the blind mole rat and the cape golden mole, two independent subterranean mammals. Forward Genomics identified several genes that are enriched in functions related to eye development and the perception of light, as well as genes involved in the circadian rhythm. These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species. Source code: https://github.com/hillerlab/ForwardGenomics/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.