Add biogeographic realm

[pbuttigieg]

@timalamenciak

Derived from #1553.

Add biogeographic realm

Note IUCN typology states the following:

The top level of the Global Ecosystem Typology divides the biosphere into five global realms: i) terrestrial; ii) subterranean; iii) freshwater (including saline water bodies on land); iv) marine; and v) the atmosphere.

[timalamenciak]

Is it possible to assign me an ID range?

Second, looking through this, there are three terms with the AP has_related_synonym X realm:
marine biome has_related_synonym "marine realm"
freshwater biome has_related_synonym "freshwater realm"
terrestrial biome has_related_synonym "terrestrial realm"

This leaves atmospheric (atmospheric layer ?) and subterranean realms to be described.

The IUCN document defines realm as follows:

One of five major components of the biosphere that differ fundamentally in ecosystem organisation and function: terrestrial, freshwater, marine, subterranean, atmospheric.

So maybe:
biogeographic realm is_a environmental system
Definition: A biogeographic realm is an environmental system with distinct ecosystem organizations and functions

[pbuttigieg]

Is it possible to assign me an ID range?

#1557

Second, looking through this, there are three terms with the AP has_related_synonym X realm: marine biome has_related_synonym "marine realm" freshwater biome has_related_synonym "freshwater realm" terrestrial biome has_related_synonym "terrestrial realm"

In those cases, the related synonym indicates that sometimes practitioners are loose with their usage of realm and biome, often using them interchangeably. This also is a flag for NLP and text mining routines, which may want to use fuzzy matching.

This shouldn't prevent is from creating true "realm" classes. We can then add comments on the synonyms on biome classes, noting why they're there and recommending use of the realm classes if that's what the practitioner really means.

Alternatively, we can take a harder line and just remove those synonyms.

This leaves atmospheric (atmospheric layer ?) and subterranean realms to be described.

Those should have their own de novo classes under "realm".

The IUCN document defines realm as follows:

One of five major components of the biosphere that differ fundamentally in ecosystem organisation and function: terrestrial, freshwater, marine, subterranean, atmospheric.

So maybe: biogeographic realm is_a environmental system Definition: A biogeographic realm is an environmental system with distinct ecosystem organizations and functions

This is an iffy definition. All ecosystem classes differ 'fundamentally' in organisation and function. Wikipedia does better, explicitly stating:

Biogeographic realms are characterized by the evolutionary history of the organisms they contain. They are distinct from biomes, also known as major habitat types, which are divisions of the Earth's surface based on life form, or the adaptation of animals, fungi, micro-organisms and plants to climatic, soil, and other conditions. Biomes are characterized by similar climax vegetation.

I'd suggest something like:

biogeographic realm =def. "An ecosystem which is surrounded by natural, macro- to megascale geographic barriers to species migration, and thus which comprises ecological communities with evolutionary histories largely delimited by those barriers."

Where the scales are from landscape ecology (see here).

With comments like: "Biogeographic realms correspond to the floristic kingdoms of botany or zoogeographic regions of zoology."

We can then link bioregions and ecoregions as cascading parts of realms (we already have ecoregions, as instances of terrestrial ecoregion)

Instances of terrestrial realms should include Udvardy's realms:

• Nearctic
• Palearctic
• Afrotropical
• Indomalayan
• Australasian
• Neotropical
• Oceanian
• Antarctic

We'll figure out how those relate to the IUCN's realms.

@thearyung - you may be interested in this and related issues, as it's a chance to interface with BIOREALM.

[pbuttigieg]

terrestrial, freshwater, marine, subterranean, atmospheric.

If these are the instances, I dont think the IUCN experts are talking about ecological realms at all. These are more general planetary compartments. This typology seems more a convenience / colloquial classification than anything grounded in ecology.

I still think we should add realm (defined accurately), and map these basic physical geography categories to their existing counterparts in ENVO.

[pbuttigieg]

Note the WWF's bioregions by realm interface here, which seems more rational.

It would make sense to me to align ENVO content on realms, bioregions, ecoregions, etc to this and link out to the instances in WWF systems. The IUCN classification can be spliced into that, as it seems more application oriented rather than fundamental.

[timalamenciak]

biogeographic realm =def. "An ecosystem which is surrounded by natural, macro- to megascale geographic barriers to species migration, and thus which comprises ecological communities with evolutionary histories largely delimited by those barriers."

This definition looks good to me. Would we then add Uvardy's realms (e.g. "Palearctic") as instances of biogeographic realm in the ontology?

There is some minor disagreement between WWF & Uvardy, which could be captured in this way.

Linking directly to the WWF bioregion by realm description page.

Would we need terms for each of the levels? (see tree diagram):

• biogeographic realm
  • subrealm
    • bioregion
      • ecoregion

You can explore each of the links above to learn more details about bioregion groupings within the 52 habitable subrealms, the unique characteristics of all 185 bioregions, and the plant and animal assemblages contained within each of the 844 component ecoregions that make up One Earth’s Bioregions Framework.

It looks like they took the 844 component ecoregions from Dinerstein et al. 2017.

There's a full table in the supplement which may be useful for our purposes: SM 1 Table 1 14Mar17.xlsx

The IUCN places its ecosystem functional groups as coming between bioregion and ecoregion in terms of scale. They reference Dinerstein:

Ecoregionalisations (e.g. Spalding et al., 2007; Abell et al., 2008; Dinerstein et al., 2017) serve as simple and accessible proxies for biotic composition based on biogeographic boundaries and have recently been shown to delineate biodiversity patterns effectively, at least on land (Smith et al., 2018).

I think the proposition of the IUCN's functional groups is that these functional arrangements can (and tend to) occur in various areas depending on micro-scale conditions (sensu landscape ecology).

Is it possible that a way forward is defining classes for subrealm, bioregion, ecosystem functional group, and ecoregion, then creating instances of these classes that correspond to terms in the WWF and IUCN taxonomies?

[pbuttigieg]

biogeographic realm =def. "An ecosystem which is surrounded by natural, macro- to megascale geographic barriers to species migration, and thus which comprises ecological communities with evolutionary histories largely delimited by those barriers."

This definition looks good to me. Would we then add Uvardy's realms (e.g. "Palearctic") as instances of biogeographic realm in the ontology?

Yes, likely as instances of "terrestrial biogeographic realm" (which we'll create alongside marine etc).

There is some minor disagreement between WWF & Uvardy, which could be captured in this way.

That's okay,- as long as the class definition holds true, we can have instances from different systems.

Linking directly to the WWF bioregion by realm description page.

Would we need terms for each of the levels? (see tree diagram):

• biogeographic realm

  • subrealm

    • bioregion

      • ecoregion

Yes, there already are ecoregions in ENVO (we should improve the definition), but bioregions and subrealms can be added. The subrealm notion bothers me a little - it again seems more of a convenience / bureaucratised grouping than anything ecological. Did you find any convincing differentia vs realm?

You can explore each of the links above to learn more details about bioregion groupings within the 52 habitable subrealms, the unique characteristics of all 185 bioregions, and the plant and animal assemblages contained within each of the 844 component ecoregions that make up One Earth’s Bioregions Framework.

It looks like they took the 844 component ecoregions from Dinerstein et al. 2017.

There's a full table in the supplement which may be useful for our purposes: SM 1 Table 1 14Mar17.xlsx

Interesting, worth analysing. Most are at the instance level, so should be easy to mint. We should cross-link those to any stable URLs that WWF provides for them.

The IUCN places its ecosystem functional groups as coming between bioregion and ecoregion in terms of scale. They reference Dinerstein:

Ecoregionalisations (e.g. Spalding et al., 2007; Abell et al., 2008; Dinerstein et al., 2017) serve as simple and accessible proxies for biotic composition based on biogeographic boundaries and have recently been shown to delineate biodiversity patterns effectively, at least on land (Smith et al., 2018).

Perhaps we should then use the Dinerstein et al material more directly.

I think the proposition of the IUCN's functional groups is that these functional arrangements can (and tend to) occur in various areas depending on micro-scale conditions (sensu landscape ecology).

Sure, but this is true of many things, so it doesn't make a good ontological class - we have to find the differntia that allow us to separate these classes from all others.

Is it possible that a way forward is defining classes for subrealm, bioregion, ecosystem functional group, and ecoregion, then creating instances of these classes that correspond to terms in the WWF and IUCN taxonomies?

Yes for all except the ecosystem functional group - we need a convincing definition of EFG that isn't also true for other classes.

[timalamenciak]

Alright, this is starting to come together I think.

biogeographic realm =def. "An ecosystem which is surrounded by natural, macro- to megascale geographic barriers to species migration, and thus which comprises ecological communities with evolutionary histories largely delimited by those barriers."

biogeographic subrealm = def. "A division of a biogeographic realm that aligns with commonly understood geopolitical and social geographic boundaries."

It seems that bioregion considers both these geographic barriers and climatic conditions, so:

bioregion = def. "An ecosystem which is delimited by natural, macro- to megascale geographic barriers to species migration and climatic conditions."`

Finally, ecoregion seems to consider biogeographic barriers, climatic conditions and species assemblage, which seems a bit too random for an ontological definition. Olson et al. 2001 (on which Dinerstein 2017 is building) defines ecoregion as follows:

"We define ecoregions as relatively large units of land containing a distinct assemblage of natural communities and species, with boundaries that approximate the original extent of natural communities prior to major land-use change."

Current ENVO definition seems to pick up on this ("distinct assemblage"):

ecoregion = current def. "A large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."

I think the question is what makes the assemblage distinct? Searching through ENVO for "assemblage" yields the term IUCN protected landscape/seascape which refers to a "historically stable assemblage." I would propose then that time and assemblage play some role in the delineation of ecoregions from one another.

ecoregion = proposed new def. "A large unit of land or water containing a geographically distinct and historically stable assemblage of species, climatic conditions and biogeographical features."

[r0sek]

@pbuttigieg side note: Frank M-K had asked how CMECS relates to the IUCN framework so I'd like to look at that as a CMECS-Ocean Decade task. CMECS uses the Spaulding Marine Ecoregions of the World (also used in WWF) Realms/Provinces/Ecoregions within US waters to define its Biogeographic Settings. But as @timalamenciak noted, IUCN is organizing biogeographic areas based on functional groups- a bottom-up approach- although I believe they are using the MEOW Ecoregion geospatial dataset to subset and inventory their Realm/Biome/Functional Group data.

[ben-norton]

Hello Everyone,
First, I created an API endpoint that returns several land cover classification systems along with the administrative divisions from a latitude and longitude coordinates. Here are several examples (you can replace the lat and long values with anything you want).
GBIF (Copenhagen)
https://geoapis.io/api/v1/services/geography/land-cover/point?lat=55.7026&lon=12.5596
Smithsonian Museum of Natural History
https://geoapis.io/api/v1/services/geography/land-cover/point?lat=38.8913&lon=-77.0261
Saguaro National Park West, Arizona
https://geoapis.io/api/v1/services/geography/land-cover/point?lat=32.2912&lon=-111.1531
Nepal
https://geoapis.io/api/v1/services/geography/land-cover/point?lat=28.4116&lon=84.1227
Hawaii
https://geoapis.io/api/v1/services/geography/land-cover/point?lat=19.5317&lon=-155.2354

I've been working off and on with various land cover classifications for more than two decades. This subject is challenging, far more challenging than I realized when I first dove into the subject.
A couple notes.

1. One of the most important aspects is spatial resolution, which is characterized in two ways.
   A. The resolution of the sensor on the remote sensing device (includes both airborne and satellite-based)
   B. The number of bands a spectral device measures. LandSat 9 has 10. ASTER has 255.
   Here, researchers develop a way to partition spectra into categories, which are labeled using some sort of ecoregion/biome category. This is very different from what you are attempting to accomplish here. (By the way, several excellent definitions are being proposed here.). I would be hesitant to go with a current scheme based on spectra rather than concepts. This is the work those projects need to better label their categories.
2. You can deduce many of the differences by reviewing the spatial resolution. This is usually buried in the methods.
3. The TEOW has a complicated background. Depending on where you look, several organizations are accredited with it. In brief, two organizations did the same activity in two ways and then published it under different names. This became abundantly clear when attempting to source each of the land cover classification systems in the API I created.
4. Uvardy was published in 1975. I'm skeptical of any system that divided the Earth's ecosystems into 193 categories in 1975. I think it was noteworthy for being the first of its kind and paved the way for future classification systems, but that is all.
5. pbuttigieg I think you explained the problem of continuity between systems very well. timalamenciak your followup is excellent. I don't think think you can map them. They weren't created with the rigors of ontologies in mind.
6. Koeppen Climate Classification is very good. I would split off climate and leave it to Koeppen. https://en.wikipedia.org/wiki/K%C3%B6ppen_climate_classification

For what it's worth, here's my recommendation. After reading through this issue, you all are clearly talented at semantics. I would put the existing system aside and define the terms as you see fit. This is the type of exercise that needs to take place. Let those systems map to you, rather than the other way around.

[ben-norton]

Also, the API queries spatial datasets in a PostGIS database. The datasets were preserved in their original state upon download. I changed column names, but didn't alter the source data in any way. They were downloaded as GDB or Shapefile > Loaded into PostgreSQL/PostGIS, then queried directly using the function:
ST_CONTAINS(geom, ST_TRANSFORM(ST_GEOMETRYFROMTEXT('POINT(".$lon." ".$lat.")', 4326),4326))
The GBIF endpoint returns a Marine Ecoregion. That doesn't make a lot of sense, but it's how the data is distributed.

[dr-shorthair]

@DavidKeith - you might want to jump in?

[pbuttigieg]

As this issue is resolved:

@ben-norton and others who have interest, I've branched off a discussion on APIs and ENVO here: #1570

@pbuttigieg side note: Frank M-K had asked how CMECS relates to the IUCN framework so I'd like to look at that as a CMECS-Ocean Decade task. CMECS uses the Spaulding Marine Ecoregions of the World (also used in WWF) Realms/Provinces/Ecoregions within US waters to define its Biogeographic Settings. But as @timalamenciak noted, IUCN is organizing biogeographic areas based on functional groups- a bottom-up approach- although I believe they are using the MEOW Ecoregion geospatial dataset to subset and inventory their Realm/Biome/Functional Group data.

@r0sek I've branched off the ecoregions issue in #1571

[pbuttigieg]

I'm closing this issue, as #1567 has been merged.

Other issues have been created for derivative tasks and discussions, noted above.