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Aloft Ecology Guide
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[EA version 0.3.3.22] Restoring the ecosystem of islands is a big part of Aloft! This is a collection of tips I've found or collected, including a Critter Guide (with pictures!).
   
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I want to acknowledge and thank Kinni for doing the initial research on all the new critters (see this post).

Corrupted Islands vs. Unhealthy Islands
Islands can have two "levels" of bad states: they can be Unhealthy, requiring certain ecological steps to restore balance*; they can also be Corrupted, having been taken over by the vile Mykter mushrooms who must be removed forcefully.

This guide covers restoration of the Unhealthy Islands. For advice on defeating the enemy on Corrupted Islands, see my Combat Guide.

* Ok, technically Unhealthy Islands may have a "Node Core" and a handful of enemies that require combat. See the Combat Guide for those, too.
Restoration Tools

The most vital tool for restoring an ecosystem is a sensitive scientific instrument, the Field Guide. While you may find one in a random container, it is much easier to just craft one. You will also need several other items in your inventory, each of which will need to occupy a slot in your hotbar:
  • Field Guide: Paper + Charcoal + Rope + Wood x2
  • Tree Seeds matching the biome
  • Flora Seeds matching the biome
  • Reishii Inocculant (make by grinding mushrooms) or Worms (EDIT: worms no longer count as decomposers; not sure when that happened)
  • Critters of various shapes and sizes (see below for Critter guide)
    • Animals (Sheep, Goats, Alpacas, and Pheasants)
    • Small Animals (like frogs, lizards, birds, and bats)
    • Insects (bees, beetles, butterflies, and moths)
Occasionally, you may need Leaf Cloth and Wood to fix a broken birdhouse (even though you don't use Leaf Cloth when building a birdhouse -- I guess you use it as binding). I never carry the cloth, so I always have to either glide back to HQ or else craft some cloth in the field (assuming the ecology has spare trees).

Field Guide Usage
Equip this on your hotbar and select it. While held, the Field Guide will highlight in red anything that needs attention to restore the ecosystem (even on distant islands). Destroy any Node Cores, chop down all the sick tress, and repair any broken birdhouses.

Read the book by holding RMB, and flip pages with LMB. There are several pages:
  • The Overview pages include the Percent Complete: how healthy the island's ecosystem is (how far you have to restore it). There are specific categories that have requirements (some islands may have 0 required, not needing that category):
    • Tree Amount* / Req'd
    • Flora Diversity / Req'd
    • Decomposer Diversity / Req'd
    • Animal Amount* / Req'd
    • Insect Diversity / Req'd
    • Small Animal Diversity / Req'd
  • Animal Amount shows how many (medium-large) animals are on the island, and gives a little picture for each.
  • Flora Diversity shows which Flora are present (while holding seeds, cycle the type with RMB)
  • Small Animal Diversity shows each type of small animal that spawns periodically on the island. Lizards appear on the ground, birds in trees, and frogs by water sources.
  • Insect Diversity shows each type of insect that spawns on the island. The flying insects are easily spotted floating mid-air, but some of the crawly insects can be hard to spot (especially the Worm). Use a Dorkip to manually scrounge them up from the ground.
* Note that this says "Amount" and not "Diversity", because you don't need several different types, you just need a certain quantity of any type. So, the other requirements want X types of flora/decomposers/insects/ect, but this requirement is only X number of trees or (medium) animals. All sheep (or goats, or pheasants) will work just fine for ecology restoration. Trees must be biome-appropriate, but can be all the same type.



Coping Without a Field Guide
While the Field Guide is quite handy, it isn't technically necessary. To restore an ecosystem without one:
  • Look for little environmental clues and hold 'E' to examine them (default binding for k+m). The text may indicate which part of the ecosystem that needs restoring.*
  • Scour the island for any sick trees or broken birdhouses; they can be more difficult to spot when they aren't highlighted red, but the trees can at least be identified readily by these characteristics: they have gnarly twists, no leaves, and pale, desiccated wood without bark. The starkest clues to a corrupted tree are deep red and black stripes of corruption creeping up the trunk.
  • Trial & error works!
    • Cycle through all the flora seeds and plant one of each (they're plentiful).
    • If you can spare it, plant some Reishii Inoculant as a test.
    • Plant tree seeds, trying to see if that restores any ecosystem health. If not, just re-collect the ineffective saplings.
    • Do the same with insects, small animals, and (medium) animals.

* You may come across small piles of bones on an unhealthy island (like the bones of a bird). These are not the same as the Bones resource that you can get in Red Cliffs (those look like they came from a much larger animal), and they will disappear once the island's flora ecology is healed (even if the island is still unhealthy in other ways). They are only present to indicate a clue towards the island's restoration.
Restoration Hints
Sometimes you can Examine something in an unhealthy ecosystem and get a clue towards one aspect of its restoration:
  • Examine a piece of wood on the ground: "The presence of decomposers would transform dead wood into rich soil" = Plant Reishii inocculant or release a Worm
  • Examine a small pile of bird bones on the ground:* "A more diverse flora would provide enough food for critters to survive" = Plant biome-specific Flora seeds
Restoring with Critters
Many islands require additional insects, small animals, or (medium) animals to achieve ecological balance. This means you need to stockpile critters if you want to restore many ecosystems. Insects are relatively easy to carry, as they stack.

Restoring with Small Animals
Small Animals are a bit challenging, as they don't stack. To keep them in bulk, you need to store them in a Vivarium ... or just leave them littered about your base.

Habitats
(TODO: more research/writing -- or else just remove the header)
Sometimes, you must build a habitat for a small animal. This must match the biome.

Restoring with (Medium) Animals
(Medium) animals require both arms and slower walking to carry, so it's best to use the animal landing pad to teleport them where you want to go. Alternately, you can position your home island directly above the destination island, carry the animal, then jump off your island onto the new one. Currently, (medium) animals don't breed, so when an island requires such an animal for restoration, you must select one of your named fur babies to tearfully part with.

Restoring with Insects
Releasing an insect will cause the island to naturally start spawning that insect, once the ecology is restored.

While Still Unhealthy
Unhealthy ecosystems deny access to their most valuable resources: <Knowledge Stones>, <Anchors>, critters, crops, and Lost Atlases. Additionally, level designers have the ability physically block anything off using thorny red & black vines.*

However, the more basic resources can be harvested still (without healing the land):
  • Anything Gathered by Hand besides crops
  • Anything Harvested by Axe -- Charcoal stumps, Wood from trees or set dressings (?)
  • Anything Harvested by Pickaxe* -- Stone, Salt, Windstone (Crystal), & Hardstone
* EXPLOIT! You can use the area of effect on the last hit of the Pickaxe's combo to harvest resources that are supposed to be blocked by black & red vines.
I'm not sure if/when they have/will patch(ed) these, but I have submitted an in-game bug report on each.

Interestingly, it looks like you can still learn from a Fresco without restoring the ecosystem.
If All Else Fails
Historically, players have had trouble with completing restoration of an island because one or more of the mykter "nodes" are unavailable for destruction (inside rock or something). If this is the case for you, you can hit F1 to open the console and type the command "killnodes".

This should only be necessary on some worlds created shortly after launch; Astrolabe has since patched this.
After The Healing
When an ecosystem is initially* restored, you get the Enthusiastic boost. This grants bonuses to move speed, attack speed, damage, and +1 Momentum. This is the best boost in the game, but it can also be stacked with all the other boosts.

* No, you can't restore and then "un-restore" an island just to get the Enthusiastic bonus again by restoring it again. You only get the boost the first time the island is restored.

Of course, the main reward for ecosystem restoration are the unlocked progression (Learning Stones and Anchors). There are also unlocked crops, and the items/passages that were made unavailable with red+black vines.
Collecting & Storing Critters
The 0.3.2 "Critters" update added a new cornucopia of fauna friends, and a few considerations must be taken when collecting these little buddies.

Note: Insects stack. Small animals (frogs, lizards, birds) do not stack.

Collecting Small Animals
There's not much to it: press 'E' to stash 'em. If you hold 'E', you will place that critter in the current hotbar slot (whatever was there is now unequipped). You don't need to equip critters, though. You can still release them from your inventory by holding 'F'.

Catching Bugs
If find yourself on a new island (healthy or unhealthy), and you look in your field guide, and you flip to the Insect Diversity page, and you notice a little buggy that you want, then you will need to either:
  • (flying) Find that bug in the world and catch it with a Bug Net
  • Bug Net: Wood + Carved Wood + Brightsun Flower + Wool Thread x2
  • (non-flying) Find that bug in the world and press 'E' to pick it up like a small animal
  • (non-flying) Dig up some soil using the Dorkip; there is a chance that you will unearth the bug. Just repeatedly dig up and place the same splotch of soil, and eventually you'll get the buggy.

Recovering Bugs
Originally posted by Ornalee:
You don't have to leave your insects and other small critters on the island. Place them down and wait a bit (go do other things to fix the ecosystem, etc.). Then check the field guide and see if the "moving in" suitcase icon has disappeared from below the animal you dropped. If it is still there, wait a bit longer, if it is gone, you can freely reclaim the critter you dropped! (And then build the appropriate habitats on the island and pick up more of the same critters, if you want to.) ːsteamhappyː


Storing Bugs and Small Animals
A Vivarium (plural "Vivaria") is used to store up to four stacks of insects or up to four individual small animals (which do not stack).

Although there is one variant of vivarium per biome per critter type, you can put vivaria of any biome on your island. (need to verify)
Kinni's List of Critters
Kinni did the initial research/list for all the insects/ small animals that can be collected (here's the original post), while I ordered & formatted it. I also found an extra critter, marked with an *asterisk.

All Biomes
Beetle:
  • Ladybug
Butterflies:
  • Orange Butterfly
  • White Butterfly
Other insects:
  • Bee
  • Worm

Emerald Isles
Bats:
  • Brown Bat (also Fallen Heights)
  • White Bat
Birds:
  • Chickadee Bird (also Fallen Heights)
  • Rainbow Bird
  • White Bird
Butterflies:
  • Dusk Brushed Butterfly
  • Free Spirit Butterfly
  • Sunset Amber Butterfly


Frog:
  • Orange Frog
Lizard:
  • Yellow Lizard


Moths: (collect at night)
  • Echoing Hopes Moth
  • Luna Green Moth
  • Pale Orange Moth
  • Moonlight Moth*

Fallen Heights
Bat:
  • Brown Bat
  • Red Bat
Beetle:
  • Blue Beetle
Birds:
  • Blue Jay
  • Chickadee (also Emerald Isles)
  • Red-Black Bird
Butterflies:
  • Crimson Dream's Butterfly
  • Queen Wisteria's Gaze (also Red Cliffs)
  • Star Doused Butterfly
  • Twilight Cloaked Butterfly
Frog:
  • Blue Frog
Lizard:
  • Purple Lizard
Moths: (collect at night)
  • Dawn Basked Moth
  • Elder's Sight Moth
  • Luna Blue Moth
  • Pale Blue Moth

Red Cliffs
Bird:
  • Black Bird
Beetle:
  • Horned Beetle
Butterflies:
  • Blazing Blossom Butterfly
  • Mist Chaser Butterfly
  • Obsidian Garbed Butterfly
  • Queen Wisterias Gaze (also Fallen Heights)
Frog:
  • Green Frog
Jerboas:
  • Brown Jerboa
  • Tan Jerboa
Lizard:
  • Green Lizard
Moths: (collect at night)
  • Ancients Whispers Moth
  • Jagged Aurora Moth
  • Purple Moth
  • Sun-Kissed Moth