publications.html

---
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permalink: /publications/
title: publications
description: Publications, CV, and external scholarly profiles.
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nav_order: 3.1
---

<h2>Publications &amp; CV</h2>

<ul>
  <li><a href="https://orcid.org/0000-0002-7398-9388">ORCID: 0000-0002-7398-9388</a></li>
  <li><a href="https://scholar.google.com/citations?user=CDY4XuYAAAAJ&amp;hl=en">Google Scholar profile</a></li>
  <li><a href="https://www.researchgate.net/profile/Brian-Enquist">ResearchGate profile</a></li>
  <li>Full CV: <a href="{{ '/cv/' | relative_url }}">View the CV page</a></li>
</ul>

<hr />

<h2>Complete Publication List</h2>

<p class="pub-intro-text">Use the tabs to group papers by subject area, or use the search box to filter within the active group.</p>

<div class="home-stats" style="max-width: 480px; margin: 0.5rem 0 1.25rem">
  <div class="home-stat">
    <span class="home-stat__number">320+</span>
    <span class="home-stat__label">Publications</span>
  </div>
  <div class="home-stat">
    <span class="home-stat__number">1993</span>
    <span class="home-stat__label">Est.</span>
  </div>
  <div class="home-stat">
    <span class="home-stat__number">12</span>
    <span class="home-stat__label">Research Areas</span>
  </div>
</div>

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<p id="pub-search-count"></p>

<p id="publication-topic-empty" class="publication-topic-empty" hidden>No publications match the current subject tab and search query.</p>

<div id="full-publication-list">{% include publications_full_from_doc.md %}</div>

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          { pattern: /traitstrap/i, weight: 3 }, // traitstrap R package
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          // Globally important plant functional traits — Kühn et al. (2021) Frontiers Biogeography
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          // Weight 3 — specific named papers requested by user
          // Bryant et al. 2008 PNAS: elevational diversity patterns across microbes and plants
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          // Neves et al. 2021 PNAS: evolutionary diversity shaped by extreme conditions
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          // Tree of life papers (Gallagher 2020, Eiserhardt 2018)
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          { pattern: /montane cloud forest/i, weight: 2 },
          // Atlantic Forest — major tropical hotspot in SE Brazil; catches Lourenco Jr et al. (2021) Ecosphere
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          // Andean forests — tropical/montane South America; catches Martínez-Villa et al. (2024) GEB
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          // Panama — tropical rainforest research system; catches Kaspari et al. (2017) Ecology
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          // Biotropica — premier Neotropical ecology journal; catches Hogan et al. (2019)
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          // Lianas — structural woody vines characteristic of tropical forests; catches Ngute et al. (2024) GCB
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          { pattern: /alpine/i, weight: 2 },
          { pattern: /tundra/i, weight: 2 },
          { pattern: /svalbard/i, weight: 2 },
          { pattern: /subalpine/i, weight: 2 },
          { pattern: /afromontane/i, weight: 2 }, // raised from 1: captures Halbritter 2025 Afromontane grasslands
          { pattern: /\bnorway\b/i, weight: 2 }, // Vandvik 2025 climate gradients in Norway
          { pattern: /\bpuna\b/i, weight: 2 }, // Halbritter 2024 Puna grasslands Peru
          { pattern: /\bmountain plant/i, weight: 2 }, // Bektaş 2024 mountain plant communities Northern Hemisphere
          // Gongga Mountains, China — high-elevation warming experiment; catches Vandvik et al. (2020) Scientific Data
          { pattern: /\bGongga\b/i, weight: 2 },
        ],
      },
      {
        id: "conservation-impacts",
        label: "Conservation Impacts",
        threshold: 2,
        matchers: [
          { pattern: /deregulation/i, weight: 2 },
          { pattern: /increasing fire|landscape fire|wildfire/i, weight: 2 },
          { pattern: /amazonian biodiversity/i, weight: 3 },
          { pattern: /drought.{0,30}biodiversity|biodiversity.{0,30}drought/i, weight: 2 },
          { pattern: /conservation planning/i, weight: 3 },
          { pattern: /conserving terrestrial biodiversity/i, weight: 3 },
          { pattern: /biodiversity, carbon and water/i, weight: 3 },
          { pattern: /areas of global importance/i, weight: 3 },
          { pattern: /balancing land use/i, weight: 3 },
          { pattern: /renewable energy/i, weight: 3 },
          { pattern: /agriculture/i, weight: 2 },
          { pattern: /extinction risk/i, weight: 3 },
          { pattern: /at risk from rapid global change/i, weight: 3 },
          { pattern: /rapid global change/i, weight: 2 },
          { pattern: /commonness of rarity/i, weight: 3 },
          { pattern: /global and future distribution of rarity/i, weight: 3 },
          { pattern: /rarity across land plants/i, weight: 2 },
          { pattern: /tree species are at risk/i, weight: 3 },
          { pattern: /protected areas?/i, weight: 3 },
          { pattern: /protected area design/i, weight: 3 },
          { pattern: /protected area selection/i, weight: 3 },
          { pattern: /spatial planning/i, weight: 2 },
          { pattern: /conservation priorit/i, weight: 2 },
          { pattern: /prioriti(s|z)ation/i, weight: 2 },
          { pattern: /biodiversity framework/i, weight: 2 },
          { pattern: /threat assessments?/i, weight: 2 },
          { pattern: /land conservation/i, weight: 2 },
          { pattern: /global change/i, weight: 1 },
          // Human pressure on tree diversity — Guo et al. (2022) PNAS
          { pattern: /\bhuman\s+(pressure|footprint|impact)\b/i, weight: 2 },
          // Climate change + land use threatening phylogenetic endemism hotspots — Guo et al. (2023) Nat. Commun.
          { pattern: /\bland\s+use\s+threat/i, weight: 2 },
          // Forest carbon stocks — Mo et al. (2024) Nat. Ecol. Evol.
          { pattern: /\bforest\s+carbon\s+stock[s]?\b/i, weight: 2 },
          // Dominance, rarity and threats in global tree communities — Hordijk et al. (2024) GEB
          { pattern: /\bpredictors\s+and\s+threat[s]?\b/i, weight: 2 },
          // Unprecedented macroclimatic exposure of tree diversity — Boonman et al. (2025) PNAS
          { pattern: /unprecedented.*macroclimatic|macroclimatic.*unprecedented/i, weight: 2 },
          // Megafauna extinction and Amazonian carbon + range reduction — Doughty et al. (2016) Ecography
          { pattern: /\bmegafauna\s+extinction\b/i, weight: 2 },
        ],
      },
      {
        id: "biodiversity",
        label: "Biodiversity",
        threshold: 2,
        matchers: [
          { pattern: /\bbiodiversity\b/i, weight: 3 },
          { pattern: /\b(beta|phylogenetic|taxonomic)\s+diversity\b/i, weight: 3 },
          { pattern: /\bfunctional\s+diversity\b/i, weight: 2 },
          { pattern: /\b(species|tree|plant|forest|bacterial)\s+diversity\b/i, weight: 2 },
          { pattern: /\bendemism\b|endemic\s+flora/i, weight: 2 },
          { pattern: /\brarity\b|\brange\s+size\b/i, weight: 2 },
          { pattern: /\bnaturalization\b|\binvasion[s]?\b/i, weight: 2 },
          { pattern: /\bcommunity\s+phylogenetics\b/i, weight: 2 },
          { pattern: /\bassemblage[s]?\b|\bcommunity\s+structure\b/i, weight: 1 },
          { pattern: /\bconserving\s+terrestrial\s+biodiversity\b/i, weight: 3 },
          { pattern: /\bthreat\s+assessments?\b|\bextinction\s+risk\b/i, weight: 2 },
          { pattern: /\bglobal\s+shortfalls?\s+in\s+threat\s+assessments?\b/i, weight: 3 },
          { pattern: /\bareas\s+of\s+global\s+importance\s+for\s+conserving\s+terrestrial\s+biodiversity\b/i, weight: 3 },
          { pattern: /\bhigh\s+exposure\s+of\s+global\s+tree\s+diversity\s+to\s+human\s+pressure\b/i, weight: 3 },
          { pattern: /\bthe\s+number\s+of\s+tree\s+species\s+on\s+earth\b/i, weight: 3 },
          { pattern: /\bglobal\s+beta[- ]?diversity\s+of\s+angiosperm\s+trees\s+is\s+shaped\s+by\s+quaternary\s+climate\s+change\b/i, weight: 3 },
          { pattern: /\bplant\s+functional\s+diversity\s+and\s+the\s+biogeography\s+of\s+biomes\s+in\s+north\s+and\s+south\s+america\b/i, weight: 3 },
          { pattern: /\bgeneral\s+patterns\s+of\s+taxonomic\s+diversity\s+and\s+biomass\s+partitioning\s+across\s+tree\s+dominated\s+communities\b/i, weight: 3 },
          { pattern: /\bthe\s+evolution\s+of\s+plant\s+communities:\s+biodiversity\s+and\s+community\s+structure\s+through\s+time\b/i, weight: 3 },
          { pattern: /\ba\s+review\s+of\s+the\s+heterogeneous\s+landscape\s+of\s+biodiversity\s+databases\b/i, weight: 3 },
          { pattern: /\bBIEN\b|biodiversity\s+informatics|botanical\s+information\s+network/i, weight: 2 },
          { pattern: /taxonomic\s+name\s+resolution\s+service|vegetation\s+inventory\s+database/i, weight: 2 },
        ],
      },
      {
        id: "biodiversity-informatics",
        label: "Biodiversity Informatics",
        threshold: 2,
        matchers: [
          { pattern: /biodiversity informatics/i, weight: 3 },
          { pattern: /\bBIEN\b/i, weight: 3 },
          { pattern: /database/i, weight: 2 },
          { pattern: /databases/i, weight: 2 },
          { pattern: /metadata/i, weight: 2 },
          { pattern: /occurrence data/i, weight: 2 },
          { pattern: /reproducible workflow/i, weight: 2 },
          { pattern: /name resolution/i, weight: 3 },
          { pattern: /cyberinfrastructure/i, weight: 2 },
          { pattern: /informatics/i, weight: 2 },
          { pattern: /thesaurus/i, weight: 3 },
          { pattern: /code sharing/i, weight: 3 },
          { pattern: /open science/i, weight: 2 },
          { pattern: /academic software/i, weight: 3 },
          { pattern: /future.{0,3}proof.*trait|trait.*future.{0,3}proof/i, weight: 3 },
          { pattern: /\bsPlot\b/i, weight: 3 },
          { pattern: /Plant-O-Matic/i, weight: 3 },
        ],
      },
      {
        id: "science-culture-teaching",
        label: "Science Culture/Teaching",
        threshold: 2,
        matchers: [
          { pattern: /scientific cultures|science of the biosphere requires the integration of scientific cultures/i, weight: 3 },
          { pattern: /science communication/i, weight: 3 },
          { pattern: /doing science in the covid|covid-19 era and beyond/i, weight: 3 },
          { pattern: /academic software development|better incentives are needed to reward academic software development/i, weight: 3 },
          { pattern: /ai chatbots can boost scientific coding|scientific coding/i, weight: 3 },
          { pattern: /teaching|field-based course|pedagogy|education/i, weight: 2 },
          { pattern: /ecological synthesis and its role in advancing knowledge/i, weight: 3 },
        ],
      },
    ];

    let activeTopic = "all";
    let navItems = null; // populated after year navigator is built

    const yearHeaders = Array.from(container.querySelectorAll("p")).filter((p) => {
      const t = p.textContent.trim();
      return /^\d{4}$/.test(t) || /^\d{4}\s*-\s*\d{4}$/.test(t);
    });

    const yearSections = yearHeaders.map((header) => {
      const lists = [];
      let node = header.nextElementSibling;
      while (
        node &&
        !(node.tagName === "P" && (/^[0-9]{4}$/.test(node.textContent.trim()) || /^[0-9]{4}\s*-\s*[0-9]{4}$/.test(node.textContent.trim())))
      ) {
        if (node.tagName === "OL" || node.tagName === "UL") {
          lists.push(node);
        }
        node = node.nextElementSibling;
      }

      const items = lists.flatMap((list) => Array.from(list.children).filter((child) => child.tagName === "LI"));
      return { header, lists, items };
    });

    function scoreTopic(text, topic) {
      let score = 0;
      for (const { pattern, weight } of topic.matchers) {
        if (pattern.test(text)) {
          score += weight;
          if (score >= topic.threshold) return score;
        }
      }
      return score;
    }

    function classifyPublication(text) {
      const matched = [];
      for (const topic of topicDefinitions) {
        if (topic.id !== "all" && scoreTopic(text, topic) >= topic.threshold) {
          matched.push(topic.id);
        }
      }
      return matched;
    }

    function getPublicationOverrides() {
      const node = document.getElementById("publication-category-overrides");
      if (!node) return [];
      try {
        const parsed = JSON.parse(node.textContent || "{}");
        return Array.isArray(parsed.overrides) ? parsed.overrides : [];
      } catch (err) {
        console.warn("Failed to parse publication category overrides:", err);
        return [];
      }
    }

    const publicationOverrides = getPublicationOverrides();

    function applyOverrideTopics(normalizedText, baseTopics) {
      const topicSet = new Set(baseTopics);
      publicationOverrides.forEach((override) => {
        const hints = Array.isArray(override.title_hints) ? override.title_hints : [];
        if (hints.length === 0) return;
        const matched = hints.some((hint) => normalizedText.includes(String(hint).toLowerCase()));
        if (!matched) return;
        const forced = Array.isArray(override.force_categories) ? override.force_categories : [];
        forced.forEach((topicId) => topicSet.add(topicId));
      });
      return Array.from(topicSet);
    }

    const allItems = yearSections.flatMap((section) => section.items);
    const topicCounts = { all: allItems.length };
    topicDefinitions.forEach((topic) => {
      if (topic.id !== "all") topicCounts[topic.id] = 0;
    });

    const itemCache = new Map();
    allItems.forEach((li) => {
      const normalizedText = li.textContent.toLowerCase().replace(/\s+/g, " ").trim();
      const autoTopics = classifyPublication(normalizedText);
      const topics = applyOverrideTopics(normalizedText, autoTopics);
      li.dataset.topics = topics.join("|");
      topics.forEach((topicId) => {
        topicCounts[topicId] += 1;
      });
      itemCache.set(li, { text: normalizedText, topicSet: new Set(topics) });
    });

    const orderedTopics = topicDefinitions.slice().sort((a, b) => {
      if (a.id === "all") return -1;
      if (b.id === "all") return 1;
      const countDiff = (topicCounts[b.id] || 0) - (topicCounts[a.id] || 0);
      if (countDiff !== 0) return countDiff;
      return a.label.localeCompare(b.label);
    });

    const tabButtons = orderedTopics.map((topic) => {
      const button = document.createElement("button");
      button.type = "button";
      button.className = "publication-topic-tab";
      button.id = `publication-topic-tab-${topic.id}`;
      button.setAttribute("role", "tab");
      button.setAttribute("aria-selected", topic.id === activeTopic ? "true" : "false");
      button.dataset.topic = topic.id;
      button.innerHTML = `${topic.label}<span class="publication-topic-count">${topicCounts[topic.id] || 0}</span>`;
      button.addEventListener("click", function () {
        activeTopic = topic.id;
        // Clear search when switching tabs so the full topic view shows
        input.value = "";
        tabButtons.forEach((tabButton) => {
          const isActive = tabButton.dataset.topic === activeTopic;
          tabButton.classList.toggle("is-active", isActive);
          tabButton.setAttribute("aria-selected", isActive ? "true" : "false");
          tabButton.style.opacity = "";
        });
        applyFilter();
      });
      tabsContainer.appendChild(button);
      return button;
    });

    tabButtons.forEach((tabButton) => {
      const isActive = tabButton.dataset.topic === activeTopic;
      tabButton.classList.toggle("is-active", isActive);
    });

    let wasSearchActive = false;

    function applyFilter() {
      const query = input.value.trim().toLowerCase();
      // When the user is searching, always search across ALL publications
      // regardless of which topic tab is active.
      const searchActive = query !== "";
      const words = searchActive ? query.split(/\s+/).filter(Boolean) : [];
      let visibleTotal = 0;
      let firstVisibleItem = null;

      // Update tab highlight: grey-out all tabs while searching (only write DOM on state change)
      if (searchActive !== wasSearchActive) {
        tabButtons.forEach((tabButton) => {
          tabButton.style.opacity = searchActive && tabButton.dataset.topic !== "all" ? "0.45" : "";
        });
        wasSearchActive = searchActive;
      }

      // Show/hide clear button
      if (clearBtn) clearBtn.hidden = !searchActive;

      yearSections.forEach((section) => {
        let visibleCount = 0;

        section.items.forEach((li) => {
          const { text, topicSet } = itemCache.get(li);
          // Require every word in the query to appear somewhere in the text
          const matchesQuery = !searchActive || words.every((w) => text.includes(w));
          // When searching, ignore topic tab and show all matching papers
          const matchesTopic = searchActive || activeTopic === "all" || topicSet.has(activeTopic);
          const match = matchesQuery && matchesTopic;
          li.style.display = match ? "" : "none";
          if (match) {
            visibleCount += 1;
            visibleTotal += 1;
            if (!firstVisibleItem) firstVisibleItem = li;
          }
        });

        section.visibleCount = visibleCount;
        section.header.style.display = visibleCount > 0 ? "" : "none";
        section.lists.forEach((list) => {
          list.style.display = visibleCount > 0 ? "" : "none";
        });
      });

      emptyState.hidden = visibleTotal !== 0;

      // Update result count
      if (resultCount) {
        if (searchActive) {
          resultCount.textContent =
            visibleTotal === 0
              ? "No papers matched your search."
              : `${visibleTotal} paper${visibleTotal === 1 ? "" : "s"} matched — scroll down to see all results.`;
        } else {
          resultCount.textContent = "";
        }
      }

      // Scroll to first visible result when searching
      if (searchActive && firstVisibleItem) {
        firstVisibleItem.scrollIntoView({ behavior: "smooth", block: "nearest" });
      }

      // Sync year nav pill visibility with current filter state
      if (navItems) {
        navItems.forEach((navItem) => {
          const section = sectionByYear.get("year-" + navItem.dataset.navYear);
          if (section) navItem.hidden = section.visibleCount === 0;
        });
      }
    }

    function debounce(fn, ms) {
      let timer;
      return function () {
        clearTimeout(timer);
        timer = setTimeout(fn, ms);
      };
    }

    input.addEventListener("input", debounce(applyFilter, 150));
    applyFilter();

    // --- Year Navigator ---
    // Stamp id + class onto each year header for anchoring and styling
    yearSections.forEach(({ header }) => {
      const year = header.textContent.trim().replace(/\s/g, "");
      header.id = "year-" + year;
      header.classList.add("pub-year-header");
    });

    // O(1) section lookup by header id (ids stamped above)
    const sectionByYear = new Map(yearSections.map((s) => [s.header.id, s]));

    // Build the sidebar rail nav
    const yearNav = document.createElement("nav");
    yearNav.id = "year-nav";
    yearNav.setAttribute("aria-label", "Jump to publication year");

    const yearNavList = document.createElement("ul");
    yearSections.forEach(({ header }) => {
      const year = header.id.replace("year-", "");
      const li = document.createElement("li");
      li.dataset.navYear = year;
      const a = document.createElement("a");
      a.href = "#" + header.id;
      a.textContent = year;
      a.addEventListener("click", (e) => {
        e.preventDefault();
        header.scrollIntoView({ behavior: "smooth", block: "start" });
      });
      li.appendChild(a);
      yearNavList.appendChild(li);
    });
    yearNav.appendChild(yearNavList);
    document.body.appendChild(yearNav);

    navItems = Array.from(yearNavList.querySelectorAll("li"));

    // Sync initial nav pill visibility with current filter state
    navItems.forEach((navItem) => {
      const section = sectionByYear.get("year-" + navItem.dataset.navYear);
      if (section) navItem.hidden = section.visibleCount === 0;
    });

    // IntersectionObserver — highlight the year currently scrolled into view
    let currentActiveNavYear = null;
    const yearObserver = new IntersectionObserver(
      (entries) => {
        const intersecting = entries.filter((e) => e.isIntersecting).sort((a, b) => a.boundingClientRect.top - b.boundingClientRect.top);
        if (intersecting.length > 0) {
          const year = intersecting[0].target.id.replace("year-", "");
          if (year !== currentActiveNavYear) {
            currentActiveNavYear = year;
            navItems.forEach((item) => {
              item.classList.toggle("is-active", item.dataset.navYear === year);
            });
          }
        }
      },
      { rootMargin: "-8% 0px -85% 0px", threshold: 0 }
    );
    yearSections.forEach(({ header }) => yearObserver.observe(header));
  });
</script>