The Hot Brook lakes of eastern Maine: a synthesis of a small-lake ecosystem, and what building a whole-lake simulation of it taught

James Cupps

Working paper, version 1.1 — 11 November 2026 (version 1.0, 29 October 2026, in US spelling). Not peer reviewed. Prepared with AI assistance (see Acknowledgments and the use of AI).

Abstract

Upper and Lower Hot Brook Lake (369 and 274 ha by the 2017 lidar; maximum depths 5.5 and 4.0 m in the 1949 survey) are two shallow, probably softwater lakes in the forested headwaters of the Penobscot basin in eastern Maine, joined by a brook about 150–200 m long. Like most small Maine lakes they are almost unstudied: apart from species lists and a few specimen records, their scientific record is one fisheries survey in August 1949. This paper assembles what is known of lakes like them — from 105 research notes on the physical limnology, nutrients, plankton, aquatic plants, fish, wildlife and forest of Maine and comparable northern lakes, each value tagged by the strength of its evidence — and reports what building and testing a whole-ecosystem simulation of the two lakes taught: a model whose fish, as individuals or schools, steer by innate habitat drives that their own neural networks bend, and grow by Fish Bioenergetics 4.0, with the year's young followed as brainless schools. The literature's only whole-lake fish counts from Maine, in three small lakes deeper than these, give standing crops of 45–117 kg/ha (the lowest a minimum); its only Maine diet data for adult chain pickerel and smallmouth bass (one 1940 survey) show white perch, not crayfish, as their main summer food; and it locates the regulation of such lakes' fish communities largely in the first year of life. Building the model exposed errors that a parameter table hides: rates that measured something else (a fertilization rate read as field egg survival, the complement of a retention formula), corrective adjustments that stacked until the pickerel killed prey at about a tenth of the rate expected from field data on pike, predation that shifted between two representations of the same fish, a weather generator plausible on average but wrong in its sequence, and an inflow right in total phosphorus but wrong in its chemical form. With its summer zooplankton, phosphorus retention and weed-bed depths near or inside their field ranges, the model still loses fish biomass each year: its young white perch stall through their first summer and fail to recruit while its predators eat down the founding stock. The measurements that would most reduce the uncertainty for these lakes and others like them are a season of water chemistry, the inflow's phosphorus by form, and a survey of the fish and their young of the year.

Keywords: Maine lakes; small shallow lakes; warmwater fish; white perch; chain pickerel; smallmouth bass; recruitment; individual-based model; bioenergetics; ecosystem model; data gaps

Contents

• Part 1: Introduction and study system (§1–2)
  • 1. Introduction
  • 2. The study system — the Hot Brook lakes and their catchment
• Part 2: Synthesis I: physics, nutrients, plankton and plants (§3.0–3.4)
  • 3. Maine lake ecosystems: a synthesis
  • 3.1 Climate, hydrology, ice and the physics of small shallow lakes
  • 3.2 Nutrients, shores and the land–lake link
  • 3.3 Plankton and the microbial loop
  • 3.4 Aquatic plants and the littoral zone
• Part 3: Synthesis II: fish, early life, predation, wildlife and forest (§3.5–3.8)
  • 3.5 The fish: community, life histories, energetics, seasonal habitat and movement
  • 3.6 Early life and recruitment
  • 3.7 Predation and the food web
  • 3.8 Wildlife, amphibians, reptiles, insects and the forest
• Part 4: The model and what building it taught (§4–5)
  • 4. The model (Methods)
  • 5. What building and testing the model taught
• Part 5: Discussion, data availability and the use of AI (§6 and back matter)
  • 6. Discussion: what is known, what is not, and what to measure
  • Data and code availability
  • Acknowledgments and the use of AI
• References
• The whole paper in one file (large: it may be slow to render on GitHub)

How to cite

Cupps, J. 2026. The Hot Brook lakes of eastern Maine: a synthesis of a small-lake ecosystem, and what building a whole-lake simulation of it taught. Working paper, version 1.1. https://github.com/jamesccupps/Reef/tree/paper-v1.1/docs/paper