PCM1: Primate Longevity Signal

PCM1 establishes the data contract reused by the later primate studies. Raw trait records and a primate phylogeny are normalized, reconciled by species, and reduced to governed derivatives before phylogenetic signal or ancestral values are interpreted.

flowchart LR
    raw["Workbook and<br/>primate tree"] --> repair["Type repair, missingness,<br/>duplicate aggregation"]
    repair --> reconcile["Tree–trait taxon<br/>reconciliation"]
    reconcile --> signal["Phylogenetic signal"]
    signal --> ancestral["Ancestral reconstruction"]

The Evidence Question In One View

Dimension	PCM1 contract
scientific object	one reconciled 75-taxon primate tree–longevity population derived from the governed workbook and tree
central idea	data repair, duplicate aggregation, pruning, and taxon reconciliation are part of the signal analysis, not clerical preparation
evidence role	establishes the reusable primate population, then compares registered signal and ancestral observations on that exact state
present conclusion	eight focused bundles are matched; the aggregate bundle is matched_with_tolerance, with 31 scalar observations split into 16 matched and 15 tolerance matches
downstream role	supplies the population and tree identity that PCM2 and PCM3 must either reuse exactly or replace with an explicit derived identity
forbidden inference	a matched preparation or signal observation does not prove figure equivalence, biological adequacy, causality, or every later primate model

PCM1 is therefore both a scientific result and the admission ledger for the primate evidence sequence. Its strongest claim is not “the files loaded”; it is that the published observations resolve through one governed preparation chain.

Read PCM1 In Two Passes

First read Data And Tree Preparation. It explains how 76 workbook rows and 77 tree tips become one ordered 75-species comparative object. Stop there if the aggregation, pruning, labels, order, or tree state is not acceptable: every later covariance and node result depends on that object.

Then read Signal And Ancestral Results. It compares the fitted λ surface, likelihood contrast, covariance entries, clade-keyed ancestral estimates, and branch summaries across the reference and Bijux implementations. Agreement in this pass establishes correspondence for those registered calculations—not biological truth, causal explanation, or general performance on other trees and traits.

The two passes answer different questions. Preparation evidence proves that both computations received the same scientific object. Result evidence proves that selected calculations on that object satisfy their declared rules. A reader needs both before citing the aggregate PCM1 verdict.

PCM1 Is A Baseline, Not A Universal Benchmark

PCM1 establishes one reusable analytical state. Later work can inherit that state only by preserving its identity or by declaring a new derived population.

Later-study condition	What PCM1 contributes	What must be established again
identical prepared CSV and tree digests	source interpretation, 75-taxon membership/order, pruning, and tree state	the later model, estimand, diagnostics, and result
same taxa with a transformed response or predictor	taxon and tree identity only	transformation, units, missingness, design matrix, and model population
subset after complete-case filtering	source lineage and candidates for admission	excluded taxa, new order, pruned tree, covariance, and derived checksums
changed tree, branch lengths, labels, or aggregation	historical context only	the entire comparative handoff and every dependent result
unrelated dataset or clade	no numerical validation transfer	complete independent admission and evidence chain

This is why PCM1 can strengthen PCM2 and PCM3 without acting as a vote for their coefficients. It removes ambiguity about inherited inputs; it does not pre-approve a new design, covariance model, or scientific conclusion.

Scientific Question

Do primate longevity traits retain phylogenetic structure after the raw table and tree are made analytically compatible, and how are reconstructed ancestral values tied to that same prepared state?

The preparation is scientifically material. Type coercion, missing-data handling, duplicate-species aggregation, pruning, and label reconciliation can change both the observations and the covariance structure used downstream.

Why The Tree Changes The Question

Species are not exchangeable replicates when related lineages share evolutionary history. Two primates with similar longevity may resemble one another partly because their branches share ancestry, so a model that treats all 75 species as independent answers a different question from a model whose covariance follows the tree.

PCM1 first establishes which 75 species and branch relationships define that dependence, then asks how strongly longevity covaries with shared history and what internal-node values follow conditionally from the fitted model. The result is about this reconciled population and tree—not an intrinsic longevity constant for all primates.

What PCM1 Contributes

PCM1 is both a scientific comparison and an admission record for later primate models. Its evidence has four distinct jobs:

Evidence role	Question answered	Bundles that own it
population evidence	which workbook rows become one row per species, and which records are excluded or aggregated?	evidence-002 through evidence-005
structural evidence	which tree, rooting, branch lengths, tips, and node identities define relatedness?	evidence-006 through evidence-008
analytical handoff evidence	which exact CSV and Newick enter signal and ancestral computation?	evidence-009
comparative result evidence	do the registered R and Bijux signal and ancestral observations correspond?	evidence-001

The roles cannot substitute for one another. A matched tree import does not establish a matched tree–trait join. A matched join does not establish a signal estimate. A matched signal estimate does not prove that the selected model is biologically sufficient.

Study Inputs

Input	Role
primate_raw.xlsx, primate.RData, primate.csv	source trait records and lecture workspace
primatetree.nex, trimmed_primatetree.nex	source and lecture-prepared phylogenies
reference_primate.csv	governed normalized trait derivative
reference_trimmed_primatetree.nwk	governed reconciled tree derivative

Input identity and provenance are recorded in the dataset catalog and provenance record.

Evidence Decomposition

Bundle	Evaluated surface	Manifest verdict
evidence-001	end-to-end study summary	matched_with_tolerance
evidence-002	workbook loading	matched
evidence-003	type repair	matched
evidence-004	missing-data accounting	matched
evidence-005	duplicate-species aggregation	matched
evidence-006	tree import	matched
evidence-007	tree diagnostics	matched
evidence-008	tree–data correspondence	matched
evidence-009	processed exports	matched

The manifest ledger is the status authority: eight focused contracts match directly, while the aggregate comparison matches under its declared numerical tolerances. Plot-only blocks remain observations about coverage, not numerical parity claims. Read the aggregate status together with its status_counts and limitations; matched_with_tolerance does not flatten those block-level distinctions.

Analytical Population Dependency Graph

flowchart LR
    workbook["evidence-002<br/>workbook load"]
    types["evidence-003<br/>type repair"]
    missing["evidence-004<br/>missingness"]
    duplicates["evidence-005<br/>species aggregation"]
    tree["evidence-006<br/>tree import"]
    diagnostics["evidence-007<br/>tree diagnostics"]
    alignment["evidence-008<br/>tree–trait alignment"]
    exports["evidence-009<br/>governed derivatives"]
    aggregate["evidence-001<br/>signal and ancestral result"]

    workbook --> types --> missing --> duplicates --> alignment
    tree --> diagnostics --> alignment
    alignment --> exports --> aggregate

The graph is the analysis population contract. A change in coercion, missingness, duplicate aggregation, tree identity, pruning, or label mapping changes the downstream population and reopens signal and ancestral evidence. The aggregate result cannot be detached from the preparation chain merely because its final taxa count remains 75.

Governed Observations

The aggregate result for the prepared 75-taxon analysis records these values:

Observation	Bijux result	Interpretation boundary
longevity range	103.0–657.6	values use the prepared source trait and its recorded units
mean longevity	317.362133	descriptive value for the reconciled taxa
estimated Pagel λ	0.803	fitted signal at the precision retained by the PCM1 aggregate record
λ=0 likelihood-ratio statistic	41.030408	comparison with the registered zero-signal model
λ=0 p-value	1.4988 × 10⁻¹⁰	model-based evidence against that registered null, not a causal result
named MRCA ancestral estimate	520.078423	conditional estimate for the five-taxon descendant signature retained in the result
branches with positive reconstructed change	72	count under the declared ancestral reconstruction
branches with reconstructed increase greater than 12	55	thresholded model output, not 55 observed evolutionary events

The source values live in bijux_reference_results.json. The aggregate scalar table contains 31 comparisons: 16 matched and 15 matched_with_tolerance. The focused preparation bundles separate workbook loading, type repair, missingness, duplicate aggregation, tree import, diagnostics, correspondence, and export so a passing headline cannot hide which transformation produced the analytical population.

Reconstruct The Verdict

Review PCM1 from dependencies to conclusion:

1. Open evidence-001/manifest.json and confirm the study, claim IDs, source locators, freshness basis, and matched_with_tolerance verdict.
2. Use inputs.manifest.json and the focused preparation bundles to establish the workbook, tree, repaired types, exclusions, aggregation, and joined taxon population.
3. Compare r_reference_results.json with bijux_reference_results.json, then inspect scalar-parity-table.json for the rule and tolerance applied to each scalar.
4. Read the block payloads and status_counts so plot-only, artifact-only, seeded-input-only, and workflow-only blocks remain outside analytical equivalence.
5. Use reviewer-summary.json and scientific_debt_register.json last; they summarize the retained records but do not replace them.

This order prevents the favorable aggregate verdict from hiding a changed input population or promoting a presentation-only block into a scientific comparison.

Citation Packet For PCM1

A citation of the signal or ancestral result should retain the PCM1 claim and bundle identifier, source and prepared input identities, 75-taxon analytical population, tree and trait derivative checksums, model and software identity, the exact result row, comparison rule and tolerance, bundle verdict, freshness, and the plotting limitation. For a branch count, also retain the eligible branch population and threshold definition; for an ancestral value, retain the descendant-taxon node key.

Do not cite the 0.803 lambda estimate from this guide alone. The guide is the interpretation route; the governed JSON observation and its manifests are the auditable record.

Interpreting The Analysis

Phylogenetic signal asks whether observed trait similarity is structured by the tree under the chosen model; it is not a measure of causal inheritance. Ancestral reconstruction estimates internal-node states conditional on the prepared tips, tree, branch lengths, and model. Neither analysis repairs a bad taxon mapping retroactively.

Signal and ancestral reconstruction also remain separate claims. Signal asks how the observed tip covariance is structured under the fitted λ model. Ancestral reconstruction estimates conditional internal-node values under a declared reconstruction model. A favorable signal test is not a validation of each ancestral estimate, and close ancestral parity is not independent support for the signal model.

Review Priorities

• Confirm that excluded and aggregated observations are enumerated.
• Confirm identical taxon sets and label normalization for traits and tree.
• Separate source-tree pruning from model-driven transformations.
• Inspect signal and ancestral outputs against the same governed derivatives.
• Treat figures as projections of recorded results, not independent evidence.

Scope

PCM1 supports the registered preparation, correspondence, export, signal, and ancestral workflow claims for this primate study family. It does not establish general performance across datasets, validate every comparative method, or close plotting equivalence beyond the declared boundary.

Continue with data and tree preparation, signal and ancestral results, or PCM2 for regression and evolutionary mode comparisons on the primate data.