AmP Ecology coding

This page presents the coding that is used in the AmP collection to specify climate, ecozone, habitat, embryo environment, migration/torpor, food, gender, and reproduction for each AmP entry. The codes are shown on the entry's results page and collected in a Matlab structure allEco.mat, which has as first-level field names the entry-names. They are used for selection of entries, linking ecological properties to DEB parameters. Food and habitat might depend on the life stage; the stage code is prepended to the habitat and food codes. The typical body temperature is specified in the mydata-files.

Lions, for instance, are viviparous, first drink milk, later eat mammals and don't migrate. They live in African grasslands and steppes, that have a dry savanna and semi-arid climate. This translates into codes (which are explained below) as:

allEco.Panthera_leo.climate = {'Am','BS'};
allEco.Panthera_leo.ecozone = {'TPa'};
allEco.Panthera_leo.habitat = {'0iTg','0iTs','0iTi'};
allEco.Panthera_leo.embryo = {'Tv'};
allEco.Panthera_leo.migrate = {};
allEco.Panthera_leo.food = {'bxM','xiCvm','xiSvm'};

Function get_eco_types of AmPtool reads this page, extracts codes and labels, and stores them in Matlab structure eco_types. View them in Matlab with e.g. global eco_types; get_eco_types; eco_types.habitat, or the label of a specific code with eco_types.climate.Dfa. The AmPtool manual explains how to use the codes in data analysis.

Life stage

A life stage is a period between two life history events. The event and life stage codes are:
event life stage
0 start of development 0b embryo (non-feeding)
b birth (start feeding) bj larva (juvenile)
x weaning/fledging bx baby (mammals), nestling (birds)
j end of acceleration jp juvenile (post larval)
p puberty pi adult
e emergence (insects) je pupa (holometabolic insects)
i death ei imago (egg-laying stage of insects)
0i total life span
In absence of metabolic acceleration, event j coincides with event b, and the juvenile stage is coded as bp. Likewise, the juvenile stages bx and xp can be catenated as bp, the post-weaning juvenile xp and adult pi stages as xi.

Climate

The climate is the pattern of variation in temperature, humidity, atmospheric pressure, wind, and precipitation, averaged over long periods of time. AmP follows the augmented Köppen-Geiger climate classification.
  • A Tropical (megathermal) climates: every month of the year with an average temperature of 18 °C or higher, with significant precipitation
    • Af Tropical rainforest climate; average precipitation of at least 60 mm in every month
    • Am Tropical monsoon climate; driest month with precipitation less than 60 mm, but more than 4 percent of the total annual precipitation
    • Aw Tropical wet savanna climate; with the driest month having precipitation less than 60 mm
    • As Tropical dry savanna climate; with the driest month having precipitation less than 4 percent of the total annual precipitation
  • B Dry (arid and semi-arid) climates: little precipitation
    • BW Dry arid climates: very little precipitation
      • BWh Hot desert climate
      • BWk Cold desert climate
      • BWn Desert climate with frequent fog
    • BS Dry semi-arid climates: little precipitation
      • BSh Hot semi-arid climate
      • BSk Cold semi-arid climate
      • BSn Semi-arid climate with frequent fog
  • C Temperate (mesothermal) climates: the coldest month averaging between 0 and 18 °C and at least one month averaging above 10 °C
    • Cf Temperate climates without dry season
      • Cfa Temperate rainy climate; coldest month averaging above −3 °C, at least one month's average temperature above 22 °C, and at least four months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled). No dry months in the summer
      • Cfb Temperate oceanic climate; coldest month averaging above 0 °C, all months with average temperatures below 22 °C, and at least four months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
      • Cfc Subpolar oceanic climate; coldest month averaging above 0 °C and 1–3 months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
    • Cw Temperate climates with dry winters
      • Cwa Monsoon-influenced humid subtropical climate; coldest month averaging above 0 °C, at least one month's average temperature above 22 °C, and at least four months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
      • Cwb Subtropical highland climate or Monsoon-influenced temperate oceanic climate; coldest month averaging above 0 °C, all months with average temperatures below 22 °C, and at least four months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
      • Cwc Cold subtropical highland climate or Monsoon-influenced subpolar oceanic climate; coldest month averaging above 0 °C and 1–3 months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
    • Cs Temperate climates with dry summer
      • Csa Hot-summer Mediterranean climate; coldest month averaging above 0 °C, at least one month's average temperature above 22 °C, and at least four months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
      • Csb Warm-summer Mediterranean climate; coldest month averaging above 0 °C, all months with average temperatures below 22 °C, and at least four months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
      • Csc Cool-summer Mediterranean climate; coldest month averaging above 0 °C and 1–3 months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
  • D Continental (microthermal) climates: at least one month averaging below −3 °C and at least one month averaging above 10 °C
    • Df Continental climates without dry season
      • Dfa Hot-summer humid continental climate; coldest month averaging below −3 °C, at least one month's average temperature above 22 °C, and at least four months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
      • Dfb Warm-summer humid continental climate; coldest month averaging below −3 °C, all months with average temperatures below 22 °C, and at least four months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
      • Dfc Subarctic climate; coldest month averaging below −3 °C and 1–3 months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
      • Dfd Extremely cold subarctic climate; coldest month averaging below −38 °C and 1–3 months averaging above 10 °C. No significant precipitation difference between seasons (neither abovementioned set of conditions fulfilled)
    • Dw Continental climates with dry winter
      • Dwa Monsoon-influenced hot-summer humid continental climate; coldest month averaging below 0 °C, at least one month's average temperature above 22 °C and at least four months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
      • Dwb Monsoon-influenced warm-summer humid continental climate; coldest month averaging below 0 °C, all months with average temperatures below 22 °C, and at least four months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
      • Dwc Monsoon-influenced subarctic climate; coldest month averaging below 0 °C and 1–3 months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
      • Dwd Monsoon-influenced extremely cold subarctic climate; coldest month averaging below −38 °C and 1–3 months averaging above 10 °C. At least ten times as much rain in the wettest month of summer as in the driest month of winter
    • Ds Continental climates with dry summer
      • Dsa Mediterranean-influenced hot-summer humid continental climate; coldest month averaging below 0 °C, average temperature of the warmest month above 22 °C and at least four months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
      • Dsb Mediterranean-influenced warm-summer humid continental climate; coldest month averaging below 0 °C, average temperature of the warmest month below 22 °C and at least four months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
      • Dsc subarctic climate; coldest month averaging below 0 °C (32 °F) and 1–3 months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
      • Dsd extremely cold, subarctic climate; coldest month averaging below −38 °C and 1–3 months averaging above 10 °C. At least three times as much precipitation in the wettest month of winter as in the driest month of summer, and driest month of summer receives less than 30 mm
  • E Polar and alpine (montane) climates: every month of the year with an average temperature below 10 °C
    • ET Tundra climate; average temperature of warmest month between 0 °C and 10 °C
    • EF Ice cap climate; eternal winter, with all 12 months of the year with average temperatures below 0 °C
  • M Marine climates
    • MA tropical: average surface temp (SST) > 25 °C
    • MB subtropical: average surface temp (SST) >15 °C, < 25 °C
    • MC temperate: average surface temp (SST) >5 °C, < 15 °C
    • ME polar: average surface temp (SST) < 5 °C

Ecozone

The ecozone is a large geographic area of the Earth's surface within which organisms have been evolving in relative isolation over long periods of time. AmP follows the augmented Udvardy ecozone classification. Terrestrial ecozones, also called biogeographic realms, include freshwater habitats. The Cape district is included in Afrotropics; New Zealand and New Guinea are included in Australasia.
  • T Terrestrial
    • TH Holarctic
      • THp Palearctic (including North Africa)
      • THn Nearctic
    • TN Neotropic (including Central America, and the Caribbean)
    • TP Paleotropic
      • TPa Afrotropic (including Cape District, Arabia)
        • TPam Madagascar
      • TPi Indomalaya
    • TA Australasia (including New Guinea, New Zealand)
      • TAz New Zealand, New Caledonia
      • TAt Tasmania
    • TO Oceania (including Polynesia (except New Zealand), Micronesia, and the Fijian Islands)
    • TS Antarctica
  • M Marine
    • MC Circumglobal oceans
    • MN Arctic ocean
    • MA Atlantic ocean
      • MAN Atlantic ocean, N
      • MANE Atlantic ocean, NE
      • MAE Atlantic ocean, E
      • MASE Atlantic ocean, SE
      • MAS Atlantic ocean, S
      • MASW Atlantic ocean, SW
      • MAW Atlantic ocean, W
      • MANW Atlantic ocean, NW
      • MAb Baltic Sea
      • MAn North Sea
      • MAm Mediterranean Sea
      • MAg Gulf of Mexico
      • MAc Carribean Sea
    • MI Indian ocean
      • MIN Indian ocean, N
      • MINE Indian ocean, NE
      • MIE Indian ocean, E
      • MISE Indian ocean, SE
      • MIS Indian ocean, S
      • MISW Indian ocean, SW
      • MIS Indian ocean, W
      • MINW Indian ocean, NW
      • MIr Red Sea
      • MIa Arabian Sea
      • MIb Bay of Bengal
    • MP Pacific ocean
      • MPN Pacific ocean, N
      • MPNE Pacific ocean, NE
      • MPE Pacific ocean, E
      • MPSE Pacific ocean, SE
      • MPS Pacific ocean, S
      • MPSW Pacific ocean, SW
      • MPW Pacific ocean, W
      • MPNW Pacific ocean, NW
      • MPb Bering Sea
      • MPy Yellow Sea
      • MPc China Sea: E, S
    • MS Southern ocean

Habitat

The habitat specifies the physical (temperature, moisture), chemical (nutrients, pH, salinity) and biological (food, predators, pathogens) surroundings in which a particular species of organism lives. The habitat codes are meant to be combined with the other codes; the life stage code is prepended to the habitat code. For birds that mainly stay on sea and breed near the coast, marine ecozones and habitats are selected. Marine bentic species might experience low temperatures in deep tropic waters.
  • T Terrestrial
    • Th shrubland (< 8 m heigh)
      • Tht tundra/high mountain vegetation (low shrubs with mosses and lichens; subsoil is permafrost)
      • Thh heathland/moorland (including short shrubs < 2 m, peatland, boglang)
      • Thf fynbos (including tall shubs > 2 m)
    • Tf forest
    • Ti savanna (grassland with patches of trees)
    • Ts steppe (grassland with some trees)
    • Tg grassland
    • Ta sparsely vegetated (semi-arid)
    • Td barely vegetated, including stony outcrops, sandy beaches
    • Tc caves
  • F Fresh water
    • Fm fresh marshes (lots of plants, stagnant or slowly moving water)
    • Fc brooks/creeks
      • Fcc brooks/creeks in caves
    • Fr rivers
    • Fl lakes
    • Fp ponds/pools
      • Fpe ephemeral ponds
    • Fe estuaries
  • S Inland salt water
    • Sl saltwater lakes
    • Sm saltwater marshes
  • M Marine
    • Mm sea or brackish marshes, regularly flooded by the tides and dominated by herbs, grasses, or shrubs, including mangroves
    • Mi intertidal zone
    • Mc marine coast (continental shelf)
      • Mcp marine coastal pelagic (neritic)
      • Mcd marine coastal demersal
      • Mcb marine coastal benthic
    • Mr reefs
    • Mp marine pelagic (benthopelagic)
      • Mpe marine epi-pelagic: 0-200 m
      • Mpm marine meso-pelagic: 200-1000 m
      • Mpb marine bathy-pelagic: 1000-4000 m
    • Md marine demersal
      • Mdb marine bathy-demersal
    • Mb marine bentic (epibentic)
    • Mv submarine vents

Embryo environment

Embryo environment specifies the local environment during the embryo stage, partly involving parental care. If differs from the habitat in concerning the immediate surroundings only. The distinction between ovovivipary (aplacental vivipary) and vivipary (placental vivipary) can be seen from the model type. A nest is a place where parents care for the embryos (brooding, including guarding, aerating, protecting); it does not need to have nest material.
  • T Terrestrial
    • Ts on soil
    • Tt burried in soil
      • Tts burrow in soil
    • Tc in dung
    • Tn terrestrial nest
      • Tnt nest in burrow in soil
        • Tntf terrestrial nest in burrow brooded by female
        • Tntm terrestrial nest in burrow brooded by male
        • Tntfm terrestrial nest in burrow brooded by female and male
      • Tns terrestrial nest on soil
        • Tnsf terrestrial nest on soil brooded by female
        • Tnsm terrestrial nest on soil brooded by male
        • Tnsfm terrestrial nest on soil brooded by female and male
      • Tnf nest on fresh water
        • Tnff nest on fresh water brooded by female
        • Tnfm nest on fresh water brooded by male
        • Tnffm nest on fresh water brooded by female and male
      • Tnp nest in shrub/tree
        • Tnpf nest in shrub/tree brooded by female
        • Tnpm nest in shrub/tree brooded by male
        • Tnpfm nest in shrub/tree brooded by female and male
        • Tnpo nest in shrub/tree brooded by host species
      • Tnw nest within tree (including caves)
        • Tnwf nest within tree brooded by female
        • Tnwm nest within tree brooded by male
        • Tnwfm nest within tree brooded by female and male
      • Tnc nest on rock/cliff (including rocky shores)
        • Tncf nest on rock/cliff brooded by female
        • Tncm nest on rock/cliff brooded by male
        • Tncfm nest on rock/cliff brooded by female and male
    • Tl terrestrial under heap of leaves
    • Th terrestrial on/in plants
      • Thl terrestrial on leaves
      • Thw terrestrial in wood/bark
    • Ta terrestrial on/in animals
    • Tv (ovo)viviparous, born terrestrial
    • Tb terrestrial brooded in pouch/mouth
      • Tbm terrestrial, brooded in pouch/mouth of male
      • Tbf terrestrial, brooded in pouch/mouth of female
      • Tbfm terrestrial, brooded in pouch/mouth of female
  • F Fresh water
    • Fp freshwater pelagic
      • Fpf freshwater floating
      • Fpe freshwater epi-pelagic
    • Fs freshwater on sediment
    • Ft freshwater burried in sediment
    • Fg freshwater on gravel
    • Fc freshwater on solid substrate
    • Fn freshwater nest
      • Fnf freshwater nest guarded by female
      • Fnm freshwater nest guarded by male
      • Fnfm freshwater nest guarded by female and male
    • Fh on/in plants in fresh water
    • Fv (ovo)viviparous, born in fresh water
    • Fb freshwater brooded in pouch/mouth
      • Fbm freshwater, brooded in pouch/mouth of male
      • Fbf freshwater, brooded in pouch/mouth of female
      • Fbb freshwater, brooded in bivalve
  • M Marine
    • Mp marine pelagic
      • Mpf marine floating
      • Mpe marine epi-pelagic
      • Mpm marine meso-pelagic
      • Mpb marine bathy-pelagic
    • Ms marine on sediment
    • Mt marine burried in sediment
    • Mc marine on solid substrate
    • Mn marine nest
      • Mnf marine nest guarded by female
      • Mnm marine nest guarded by male
      • Mnfm marine nest guarded by female and male
    • Mb marine, brooded in pouch/mouth
      • Mbm marine, brooded in pouch of male
      • Mbf marine, brooded in pouch of female
    • Mv (ovo)viviparous, born in marine water

Migration/Torpor

Migration (seasonal movement from one region to another) and torpor (seasonal partial metabolic shutdown) are both responses to local shortage of food. Empty code means no migration or torpor. For migrating species, habitat and ecozone refer to breeding area.

Migration

  • Mo oceanodromous: live and migrate wholly in the sea
  • Mp potamodromous: live and migrate wholly within fresh water
  • Ma amphidromous: migrate from fresh water to the sea, or vice versa, but not for the purpose of breeding
  • Md diadromous: migrate between the sea and fresh water
    • Mda anadromous: migrate from the sea up into fresh water to spawn
    • Mdc catadromous: migrate from fresh water down into the sea to spawn
  • Ms short-distance migration, only affecting the extreme parts of the breeding grounds
  • Ml long-distance migration, affecting all breeding grounds
Torpor
  • TT Seasonal temperature induced: hybernation
  • TW Seasonal water induced: dry season

Food

The life stage code is prepended to the food code.
  • A symbiontic
    • Aa algal symbionts
    • Ab bacterial symbionts
  • D detrivore (bacteria, small fungi, organic matter)
    • Dc coprovore (faeces)
  • B bacterivore (including micro-organisms)
  • P planktivore (small aquatic organisms, macro-movement controlled by flow, not by swimming)
    • Pn nano-planktivore (including bacteria)
    • Pp phyto-planktivore
    • Pz zoo-planktivore
  • O omnivore (plants/animals/fungi)
  • H herbivore (plants)
    • Hr roots/tubers
    • Hl shoots/leaves
      • Hlf fermented shoots/leaves
    • Hs seeds/berries/fruits
    • Hn nectar/pollen
    • Hw wood/bark
    • He exudates/sap
    • Ha algae
  • F fungivore
  • C carnivore (living animals)
    • Ci living invertebrates
      • Cis living sponges
      • Cia living sea anamones/corals
      • Cih living hydrozoans
      • Cij living jelly fish
      • Cin living ctenophores
      • Cir living rotifers
      • Ciw living annelids
      • Cim living molluscs
      • Cic living cephalopods
      • Cid living decapods
      • Cik living planktontic crustaceans (e.g. copepods/krill)
      • Cii living insects
      • Cie living echinoderms
      • Cit living tunicates
    • Cv living vertebrates
      • Cvf living fish
      • Cva living amphibians
      • Cvr living reptiles
      • Cvb living birds
        • Cvbe bird eggs
      • Cvm living mammals
  • M milk
  • E coprophagy
  • S scavenger (dead animals)
    • Si dead invertebrates
      • Sia dead sea anamones
      • Sij dead jelly fish
      • Sim dead molluscs
      • Sic dead cephalopods
      • Sii dead insects
      • Sie dead echinoderms
    • Sv dead vertebrates
      • Svf dead fish
      • Sva dead amphibians
      • Svr dead reptiles
      • Svb dead birds
      • Svm dead mammals
  • T parasitic (animal tissue)
    • Ti tissue of invertebrates
      • Tia tissue of sea anamones
      • Tij tissue of jelly fish
      • Tim tissue of molluscs
      • Tic tissue of cephalopods
      • Tii tissue of insects
      • Tie tissue of echinoderms
    • Tv tissue of vertebrates
      • Tvf tissue of fish
      • Tva tissue of amphibians
      • Tvr tissue of reptiles
      • Tvb tissue of birds
      • Tvm tissue of mammals

Gender

Simultaneaus hermaphrodites have a reduced reproduction efficieny kap_R (for egg production), to accomodate allocation to sperm production.
  • H hermaphrodite (both male and female)
    • Hh simultaneous hermaphrodite
    • Hs sequential hermaphrodite
      • Hsf protogenic hermaphrodite (first female, then male)
        • Hsff protogenic hermaphrodite (first female, then male), with full females (no full males)
      • Hsm protandric hermaphrodite (first male, then female)
        • Hsmm protandric hermaphrodite (first male, then female), with full males (no full females)
      • Hsb bidirectional hermaphrodite
  • D dioecy (either male or female, also called gonochoric)
    • Dt gender determined by temperature
      • Dtfm low temperature females, high temperature males
      • Dtmf low temperature males, high temperature females
    • Dg gender determined by genetics
    • Da normally gonochoric, but accidentally hermaphroditic

Reproduction

Most animal species have a single generation (female, male, hermaphrodite), but others alternate generations, e.g. between sexual or asexual, known as heterogamy. Many parasites change host, while changing generations.
  • A heterogamy (alternating generations)
    • Aa alternating sexual and asexual (budding) generations
    • Ab alternating sexual and non-sexual stages involving changing of hosts
    • Ap parthenogenesis (diploid females get dipoid daughters without fertilisation)
      • Apa accidental parthenogenesis (mostly homogamous)
      • Apf facultative parthenogenesis (males sometimes present, cyclic parthenogenesis)
      • Apo obligate parthenogenesis (males absent or no gene donation)
  • O homogamy (no alternating generations, fertilisation obligatory)
    • Ob simultaneous sexual and asexual (budding) reproduction