Add Phylogenetic Ecology tab to publications page [2026-05-13]

Author: benquist

_pages/publications.html

@@ -251,6 +251,39 @@ <h2>Complete Publication List</h2>
 					{ pattern: /rarity/i, weight: 1 },
 					{ pattern: /broad geographic/i, weight: 2 },
 					{ pattern: /continental/i, weight: 1 },
+					// Species abundance distributions — McGill et al. 2007; Morlon et al. 2009
+					{ pattern: /species\s+abundance\s+distribution[s]?/i, weight: 3 },
+					{ pattern: /abundance\s+distribution[s]?\b/i, weight: 2 },
+					// Macroscopic patterns — Enquist et al. 2002 (Science)
+					{ pattern: /macroscopic\s+patterns?/i, weight: 3 },
+					// Global rarity — Enquist et al. 2019 (Science Advances)
+					{ pattern: /global.*rarity|rarity.*global/i, weight: 2 },
+					// Northern/Southern Hemisphere breadth — Bektaş et al. 2024 (Ecography)
+					{ pattern: /northern\s+hemisphere|southern\s+hemisphere/i, weight: 2 },
+					// Latitudinal diversity gradient — Lamanna et al. 2014; Weiser et al. 2017
+					{ pattern: /latitudinal\s+diversity\s+gradient/i, weight: 3 },
+					// Diversity gradients — Weiser et al. 2018; Stegen et al. 2012
+					{ pattern: /diversity\s+gradient[s]?/i, weight: 2 },
+					// Biodiversity patterns across gradients — Stegen et al. 2012
+					{ pattern: /biodiversity\s+patterns?\s+(across|along)/i, weight: 2 },
+					// Species–energy relationship — Símová et al. 2011
+					{ pattern: /species[- ]energy\s+relationship/i, weight: 3 },
+					// General laws of biodiversity — Moulatlet et al. 2025
+					{ pattern: /general\s+laws?\s+of\s+biodiversity/i, weight: 3 },
+					// Global beta-diversity — Xu et al. 2023
+					{ pattern: /global\s+beta[- ]?diversity/i, weight: 2 },
+					// Global distribution and drivers (trait geography) — Mo et al. 2024
+					{ pattern: /global\s+distribution\s+(and\s+)?drivers?/i, weight: 2 },
+					// Across the globe — Hordijk et al. 2024
+					{ pattern: /across\s+the\s+globe/i, weight: 2 },
+					// Body size–abundance — White et al. 2007; Dillon et al. 2019
+					{ pattern: /body\s+size.{0,20}abundance/i, weight: 2 },
+					// Broad climatic gradients — Stegen et al. 2011
+					{ pattern: /broad\s+climatic\s+gradient[s]?/i, weight: 2 },
+					// Global productivity–richness — Hordijk et al. 2023
+					{ pattern: /global\s+relationship.*richness|richness.*global\s+relationship/i, weight: 2 },
+					// Tree diversity / species under global change — Boonman et al. 2024
+					{ pattern: /tree\s+species.*global\s+change|global\s+change.*tree\s+species/i, weight: 2 },
 				],
 			},
 			{
@@ -315,6 +348,20 @@ <h2>Complete Publication List</h2>
 					{ pattern: /intraspecific variation/i, weight: 1 },
 					{ pattern: /leaf mass per area/i, weight: 1 },
 					{ pattern: /\btraits\b/i, weight: 1 },
+					// Enquist et al. 1999 — Allometric scaling of production and life history variation in vascular plants (Nature 401)
+					{ pattern: /life history variation/i, weight: 2 },
+					// West et al. 1999 — A general model for the structure, and allometry of plant vascular systems (Nature 400)
+					{ pattern: /vascular systems/i, weight: 2 },
+					// Wood density as a key plant functional trait (Mo 2024, Stegen 2009, Swenson 2007–2008)
+					{ pattern: /wood density/i, weight: 2 },
+					{ pattern: /wood specific gravity/i, weight: 2 },
+					// Functional composition papers (Swenson 2020, Martínez-Villa 2024, Enquist 2011)
+					{ pattern: /functional composition/i, weight: 2 },
+					// Life-history scaling in trait context (Grady 2024)
+					{ pattern: /life history scaling/i, weight: 2 },
+					// Rebuilding community ecology from functional traits (McGill et al. 2006) — already caught by /functional trait/i
+					// Leaf size/area as a functional trait proxy (Li 2020)
+					{ pattern: /leaf size.*ecosystem|ecosystem.*leaf size/i, weight: 2 },
 				],
 			},
 			{
@@ -356,6 +403,28 @@ <h2>Complete Publication List</h2>
 					{ pattern: /evenness/i, weight: 1 },
 				],
 			},
+			{
+				id: 'phylogenetic-ecology',
+				label: 'Phylogenetic Ecology',
+				threshold: 2,
+				matchers: [
+					// Weight 3 — specific, diagnostic community-phylogenetics terms
+					{ pattern: /community phylogenetics/i, weight: 3 },
+					{ pattern: /phylogenetic (diversity|endemism|signal|relatedness|beta diversity)/i, weight: 3 },
+					{ pattern: /phylogenetic.{0,20}(community|assembly) (ecology|structure)/i, weight: 3 },
+					{ pattern: /(community|functional).{0,20}phylogenetic (structure|composition)/i, weight: 3 },
+					{ pattern: /scale depend\w+ .{0,20}phylogenet/i, weight: 3 },
+					// Weight 2 — "phylogenetic" or "phylogeny" anywhere (title, journal, methods)
+					{ pattern: /phylogeneti/i, weight: 2 },
+					// Weight 1 — weak signals; two together reach threshold
+					// Swenson collaboration spans community phylogenetics, trait-phylogeny, and assembly
+					{ pattern: /swenson/i, weight: 1 },
+					{ pattern: /eco-evolutionary/i, weight: 1 },
+					{ pattern: /evolutionary determinants/i, weight: 1 },
+					{ pattern: /opposing assembly mechanisms/i, weight: 1 },
+					{ pattern: /null model.{0,20}community|community.{0,20}null model/i, weight: 1 },
+				],
+			},
 			{
 				id: 'tropical-ecology',
 				label: 'Tropical Ecology',

chat_provenance_log.md

@@ -270,3 +270,8 @@ Outcome: Full rewrite of _pages/gallery.md. Removed ~55 low-quality/misplaced/un
 ## 2026-05-09 — Fix about page text overflow
 Prompt: Text spacing/justification for https://enquistlab.github.io/about/ runs off the page. Standardize to other tabs and layout.
 Action: Removed 100vw full-bleed breakout (width:100vw;left:50%;margin-left:-50vw) from .about-article in _sass/_lab-redesign.scss. The 100vw value includes the scrollbar width causing horizontal overflow. About page now stays within the standard 930px .container like all other pages. Profile image column narrowed from 300px to 260px to fit cleanly. Committed and pushed.
+
+## 2026-05-13 — Add Phylogenetic Ecology tab to publications page
+Prompt: "For enquistlab.github.io/publications/ I would like to add another tab under 'phylogenetic ecology'. Include many of the papers with Nate Swenson, Nathan Kraft, as well as other papers coauthored with Jessica Green."
+Action: Added `phylogenetic-ecology` entry to the `topicDefinitions` array in `_pages/publications.html`, inserted after the 'Functional Ecology' tab. The phylogenetics-comparative-agent reviewed the candidate papers (Swenson, Kraft, Green collaborations) and rated each for phylogenetic centrality. Final matchers: weight-3 for community phylogenetics, phylogenetic diversity/endemism/signal/structure, and scale-dependency; weight-2 for any 'phylogeneti' token; weight-1 weak signals (swenson, eco-evolutionary, opposing assembly mechanisms) that pair to reach threshold=2. Green papers (SADs, theory, microbes) were classified as macroecology — not included in this tab. Commits pending.
+**Agent:** m → phylogenetics-comparative-agent → direct edit