Molecular Ecology

Molecular Ecology (molecular-ecology)

Journal positioning

Molecular Ecology is a Wiley journal and the flagship venue for work that uses molecular tools to answer ecological, evolutionary, and conservation questions. Its defining character is the integration of molecular data with a genuine ecological or evolutionary question: the molecular method is the means, not the end. The journal rewards population genomics, phylogeography, landscape genetics, molecular adaptation, eDNA and metabarcoding, host-microbe and community molecular ecology, and conservation genomics — provided the study is hypothesis-driven and the biological interpretation is as strong as the genetic analysis. It is not a venue for marker-development notes, methods without a biological question, or descriptive genotyping without ecological inference. Readership spans molecular ecologists, evolutionary geneticists, and conservation biologists. This skill is a fit / venue-selection / re-framing tool. It does not replace the journal's current official guidelines. Before submitting, re-check the live author instructions on the Molecular Ecology Wiley site.

When to trigger

• The author names Molecular Ecology as the target for a study applying molecular or genomic data to an ecological, evolutionary, or conservation question.
• A population-genomics, phylogeography, eDNA, or landscape-genetics manuscript is choosing between Molecular Ecology, Molecular Biology and Evolution, and Nature Ecology & Evolution.
• A study has strong molecular data but the author needs to confirm the ecological/evolutionary question is framed sharply enough for this venue.
• The author needs Molecular Ecology's data-archiving, reproducibility, and scope conventions, plus desk-reject criteria, before submission.

Scope & topic fit

• Population genomics and landscape genetics: structure, gene flow, demographic history, and adaptation across landscapes inferred from genome-wide data.
• Phylogeography: the geographic distribution of genealogical lineages and the historical processes — refugia, colonization, vicariance — that produced them.
• Molecular adaptation and selection: genome scans, environmental-association analyses, and functional links between genotype, phenotype, and environment.
• Environmental DNA, metabarcoding, and community molecular ecology: biodiversity assessment, species detection, and community composition from molecular data with ecological inference.
• Host-microbe and symbiosis ecology: microbiome structure and function analyzed in an ecological or evolutionary framework.
• Conservation genomics: effective population size, inbreeding, hybridization, units of conservation, and adaptive capacity informing management.

Method & evidence bar

• The ecological or evolutionary question must drive the study; molecular data are evidence toward a hypothesis, not the result in themselves.
• Sampling design must support the inference: population/site replication, sample sizes, and geographic or temporal coverage adequate for the claims.
• Genomic analyses must be current and appropriate — suitable marker density or sequencing depth, correct population-genetic models, and attention to confounders such as population structure, linkage, and ascertainment bias.
• Statistical support is expected: model comparison, demographic-inference validation, simulation or resampling where relevant, and honest treatment of uncertainty.
• Bioinformatic pipelines must be reproducible: software versions, parameters, and filtering steps reported; custom code deposited.
• Raw sequence data and genotype/processed datasets must be archived in appropriate public repositories (e.g., NCBI SRA/GenBank, Dryad/Zenodo) per current policy.

Structure & house style

• Molecular Ecology publishes full-length research articles; re-check current article types, length, and figure limits on the live site.
• The Introduction must establish the ecological/evolutionary question and hypotheses before the molecular approach; Methods document sampling, lab/sequencing, and bioinformatics in reproducible detail.
• Results should integrate genetic patterns with biological interpretation rather than presenting genotype summaries in isolation; the Discussion must return to the opening question.
• Figures favor informative population-genetic visualizations — structure plots, ordinations, maps, demographic models — each carrying a clear inference.
• Extensive bioinformatic detail, parameter tables, and supplementary analyses belong in Supporting Information; the main text stays focused on the question.
• A clear data-accessibility statement with all repository accessions is a standard required element; confirm the current format.

Official-submission checklist

• Before giving submission-ready advice, read ../../resources/source-basis.md and ../../resources/official-source-map.md; start from the official source anchors for this journal family, then cite the current journal-specific page you checked.
• Search the live site for "Molecular Ecology author guidelines" and follow the current Wiley version.
• Re-check current article types, length and figure limits, and any distinction between full articles and shorter formats.
• Re-check the data-accessibility policy: required repositories for raw sequence data, genotypes, and code, plus the data-accessibility-statement format.
• Re-check competing-interests, funding, ethics/permits (sampling, CITES), and AI-use disclosure requirements; confirm preprint policy (bioRxiv/EcoEvoRxiv generally compatible).
• If the live official instructions conflict with this skill, the official instructions win.

Pre-submission self-check

• One sentence — the ecological or evolutionary question driving the study and how the molecular data answer it.
• The molecular method is a means to a biological inference, not the manuscript's main result.
• Sampling design and sample sizes support the population-genetic or phylogeographic claims.
• Bioinformatic pipeline is reproducible: versions, parameters, and filtering reported.
• Raw sequence data, processed datasets, and code are archived with accessions ready.
• Required collection/export permits and ethics approvals are documented.

Common desk-reject triggers

• A marker-development, primer, or genotyping-protocol note without an ecological or evolutionary question.
• Descriptive population genotyping that reports structure or diversity statistics without testing a hypothesis or drawing ecological inference.
• A study whose sampling design (too few populations, too few individuals) cannot support its demographic or selection claims.
• A microbiome or eDNA dataset presented as a species/taxa list without ecological or evolutionary interpretation.
• A genomics-heavy paper whose biological question is generic, post hoc, or weakly connected to the molecular results.

Re-routing decision

• Molecular-evolutionary or phylogenetic methodology and molecular-evolution theory at the core: Molecular Biology and Evolution (molecular-biology-and-evolution).
• A conceptually broad eco-evolutionary advance of general significance beyond the molecular-ecology community: Nature Ecology & Evolution (nature-ecology-and-evolution).
• A concise conceptual advance integrating theory and data: Ecology Letters (ecology-letters).
• A primarily bioinformatic method or software tool: a methods venue (e.g., Methods in Ecology and Evolution, Molecular Ecology Resources).

Output format

[Fit] High / Medium / Low (one-line reason)
[Target] Molecular Ecology
[Topic tags] <2–3 closest topics>
[Method/evidence] <does a sharp ecological/evolutionary question drive molecular data with adequate sampling, current analyses, and reproducible pipelines?>
[Top risk] <the single most likely reason for rejection>
[Official items to re-check] <article types/limits / data-accessibility repositories / permits-ethics / disclosure / preprint policy>
[Re-route suggestion] <if not a fit, a better-matched venue>

Source: brycewang-stanford/Awesome-Journal-Skills → English-NaturalScience-Journal-Skills/skills/molecular-ecology/SKILL.md