Lichens of southern Africa's 일지

https://archive.bgbm.org/BGBM/STAFF/Wiss/Sipman/keys/Afroxantkey3a.pdf

Compiled Key to Xanthoparmelia in Southern Africa
by H. Sipman, 25 Nov. 2017
The key is based on the keys for the genera Karoowia, Paraparmelia, Xanthoparmelia and the Neofuscelia group published by Hale (1989), Elix (201), Hale (1990) and Esslinger (1977), respectively. The species not known from Southern Africa are omitted, some rearrangements are made, and added are all additional species reported by Fryday (2015) in the Checklist for South Africa. For the added species a reference to a description is given; for the other species descriptions can be found in the above publications. The delimitation of the genus Xanthoparmelia follows Blanco et al. (2004). Genus abbreviations: K = Karoowia; N = Neofuscelia; P = Parmelia; Par = Paraparmelia; X = Xanthoparmelia. For the currently accepted name of the species, see the websites of Index Fungorum or Mycobank.

Key to main groups (coinciding largely with former genera)

1. Thallus loosely adnate, attached by central umbicilus.................................................. Xanthomaculina
   1' Thallus loosely or tightly adnate, attached by rhizines or scattered hapters ... goto 2

2. Thallus upper surface with pseudocyphellae .................................................................. Namakwa
   2' Thallus upper surface without pseudocyphellae ... goto 3

3. Thallus upper cortex with atranorin or usnic acid, colour whitish-, yellowish- or greenish grey ... goto 4
   3' Thallus upper cortex without atranorin or usnic acid; thallus colour dark brownish grey. ... goto 6

4. Thallus upper cortex with atranorin, upper surface whitish grey, K + pale yellow ........... Paraparmelia
   4' Thallus upper cortex with usnic acid, upper surface yellowish to greenish grey, K - ... goto 5

5. Thallus tightly adnate, subcrustose, often with immersed (aspicilioid) apothecia, with dull upper surface without or with thin epicortex ...... Karoowia
   5' Thallus tightly or loosely adnate, subcrustose or foliose to pulvinate, with sessile apothecia with constrated base, usually with glossy upper surface at least near the lobe tips, occasionally pruinose to scabrose. .... (Xanthoparmelia) ... goto 7

6. Thallus subfruticose, with linear, erect to spreading, not adnate lobes................ Almbornia
   6' Thallus foliose to subcrustose, with shorter, subirregular to sublinear, loosely to tightly adnate lobes .... Neofuscelia

7. Thallus upper surface dull, at the lobe tips coarse-pruinose .................... Pruinose Xanthoparmelia
   7' Thallus upper surface shiny, at least at the lobe tips, rarely thinly white-pruinose.. ... goto 8

8. Thallus sorediate........................................................................................... Sorediate Xanthoparmelia
   8' Thallus not sorediate ... goto 9

9. Thallus terricolous (on soil, humus or pebbles, attached or vagrant) .... Terricolous Xanthoparmelia
   9' Thallus saxicolous, rarely on other substrate ... goto 10

10. Thallus isidiate ... goto .11
    10' Thallus not isidiate . ... goto 12

11. Thallus with pale brown to brown lower surface, darkest at the tips .......Isidiate Xanthoparmelia pale below
    11' Thallus with black lower surface, paler at the tips ....................................... Isidiate Xanthoparmelia black below

12. Thallus with pale brown to brown lower surface, darkest at the tips ........ Nonisidiate, Nonsorediate Xanthoparmelia pale below
    12' Thallus with black lower surface, paler at the tips ......................................... Nonisidiate, Nonsorediate Xanthoparmelia black below

see article for keys for the different groupings.

On iNaturalist we already have a field

Lichen substrate

Substance lichen is growing on. Please use "Host" field to designate species of a living substrate.
https://www.inaturalist.org/observation_fields/189
Allowed values:
unknown 952
bark 6513
wood 713
moss 182
rock 2797
soil 365
leaves 227
artifact 151
bone 13
animal 18

also:

Fungi and Lichen: Substrate

What is the fungus or lichen growing on or in?
https://www.inaturalist.org/observation_fields/11447
Allowed values:
na 7825
soil 467
rock 49
wood and leaf litter 438
unsure 41

There are other fields (lots related to Lichens, many duplicates - see https://www.inaturalist.org/observation_fields?commit=Search&page=2&q=lichen&utf8=%E2%9C%93)

However, it seems that surely the substrate "Rock" (and indeed soil?) is probably crucial - as important as the category rock itself.

There are several "open" fields for Rock Type, but these are problematic. Under geology, we have several, but none are comprehensive (and how comprehensive do we need to be?).
https://www.inaturalist.org/observation_fields/319
https://www.inaturalist.org/observation_fields/2753
https://www.inaturalist.org/observation_fields/7443 (Protea Atlas & CREW - s Afr)

respectively these are:

• Not Applicable: 269 | 0 | 0
• Unknown: 0 | 23 | 12
• Other: 0 | 3 | 24

Sandstone: 202 | 62 | 831
Tertiary Sands: 0 | 0 | 150 Applicable to geology? But Namib Desert!
Limestone 11 | 5 | 66
Shale: 0 | 1 | 65
Granite 0 | 0 | 25
Ferricrete: - | - | 13
Silcrete: - | - | 12 How does one distinguish this from Ferricrete - merge?
Silt-clay-stone 11 | - | - What does this mean - scrap!
Quartzite 0 | 4 | 7 But is it really so easy to tell "sandstone" from "quartzite" - and what about Quartz?
Conglomerate: - | - | 9 Rather code for the constituent geology, unless not specific?
Dolerite: 0 | 0 | 7
Basalt 3 | 2 | 1
Alluvials - | 2 | - What does this mean? (either soil or sand/conglomerate) - scrap!
Dolomite 0 | - | -
Serpentine 0 | - | -

Others (not used in any projects) - these seem to be superfluous (some being metamorphosed versions of the above)
Volcanic
Schist
Gneiss
Marble
Chert
Chalk
Gypsum
Andesite
Diorite
Ultrabasics

Your thoughts??

Identifying Lichens on iNaturalist

1. Do not identify without the required identification characteristics.
   Ask the user for additional missing characters before making an ID.
   Identify only to the rank warranted by the features available.

2. Submit a comment without an ID if you are uncertain of an identification.
   Explain what features are precluding the ID.

3. Justify Disagreements.
   Provide reasons if you disagree with an existing ID or suggestion. This allows others to asses the validity of the reasons. Without reasons it is impossible to evaluate disagreements.

4. Also justify an Agreement.
   Leave a comment on why you are agreeing.

< added: >

1. !! Never use data for research that you have not checked the IDs for yourself, or had a specialist check for you.
   
2. !! If you are specialist, annotate your IDs liberally - they will be useful for training future lichenologists.
3. !! When vetting data for research, be sure to annotate issues on the source data: do not just discard or disregard data when you are suspicious as to its quality.

< and: >

1. Look out or unusual or rare species or complexes on submitted observations.
   If useful, suggest to the observer to duplicate (or triplicate) the observation to ID those species.

< P.S. >

• !! Learn how to use the Identification Curation tool on iNaturalist. Use it to manage your workflow.
  Two-minute tutorial here: learn it:: https://vimeo.com/246153496

from:
R. Troy McMullin and Jessica L. Allen (2022) An assessment of data accuracy and best practice recommendations for observations of lichens and other taxonomically difficult taxa on iNaturalist. Botany 100: 491–497 https://dx.doi.org/10.1139/cjb-2021-0160

Recommendations for making lichen observations on iNaturalist that will be identifiable!

1. Become familiar with the iNaturalist platform.
   This applies to both contributors and researchers.

2. Take clear, well-lit pictures.
   Quality is essential. Must be in focus. Light balance and colour must be good. Take many pictures, discard poor quality. Post-process pictures.

3. Consider your photographical equipment.
   Cellular phones: augment with hand lenses for magnification. Use tripods and stabilizing devices.
   Cameras: use tripod and timed delay.

4. Take multiple pictures of relevant structures at multiple magnifications from all angles.
   usually includes (a) the entire individual from a distance (b) multiple close-ups of reproductive structures from different angles (c) also include pictures of the lower surface, or other hidden parts.

5. Record what the species is growing on or in.
   Substrate information is often as important as a picture for identification.

6. Include microscope images and chemical tests.
   Photograph through a microscope, or photograph the chemical tests.

7. Add extensive notes.
   include substrate, habitat, descriptions of hidden characters, measurements of microscopic characters (spores, etc.), outcomes of chemical tests.

8. Limit the amount of disturbance.
   Some species require collection for ID: Get permits. Collect the minimum. Deposit vouchers in herbaria.
   (or accept that ID to family, genus or complex is fine).

9. Avoid immature individuals.
   These often cannot be identified, as reproductive organs are invariably needed.

10. Obscure locality data for rare species.
    (iNat does this automatically for sensitive species, and we have no known sensitive lichens on the subcontinent)

11. Limit reliance on machine generated identifications.
    (esp. where specialists have not vetted IDs and thus helped train the AI). Beware of identifying finer than possible.

from:
R. Troy McMullin and Jessica L. Allen (2022) An assessment of data accuracy and best practice recommendations for observations of lichens and other taxonomically difficult taxa on iNaturalist. Botany 100: 491–497 https://dx.doi.org/10.1139/cjb-2021-0160

Two nice articles on using Lichen data from iNaturalist - both are open access:

Munzi S, Isocrono D and Ravera S (2023) Can we trust iNaturalist in lichenology? Evaluating the effectiveness and reliability of artificial intelligence in lichen identification. Lichenologist 55, 193–201. https://doi.org/10.1017/S0024282923000403

Abstract
iNaturalist is a widely-utilized platform for data collection and sharing among non-professional volunteers and is widely employed in citizen science. This platform’s data are also used in scientific studies for a wide range of purposes, including tracking changes in species distribution, monitoring the spread of alien-invasive species, and assessing the impacts of urbanization and land-use change on biodiversity. Lichens, due to their year-round presence on trees, soil and rocks, and their diverse shapes and colours, have captured the attention of iNaturalist users, and lichen records are widely represented on the platform. However, due to the complexity of lichen identification,
the use of data collected by untrained, or poorly trained volunteers in scientific investigation poses concerns among lichenologists. To address these concerns, this study assessed the reliability of lichen identification by iNaturalist users by comparing records on the platform with identifications carried out by experts (experienced lichenologists) in three cities where citizen science projects were developed. Results of this study caution against the use of unchecked data obtained from the platform in lichenology, demonstrating substantial inconsistency between results gathered by iNaturalist users and experts.

It is worth pointing out that no competent researcher would use data (whether from a CS site like iNaturalist, or even a herbarium like our national herbarium PRE) without checking the data first. There are several steps to this, but these involve identification, taxa that can be confused, location errors, outliers, and other checks. In this regard this paper is rather naive.
The recommendations are good though: a higher level for RG (more agreements), additional agreements contributing to surety. (iNat counts agreements and disagreements, so this is useful. They stopped though at weighting experts more. Their ideas on the CV AI identifications ignores the fact that the AI is trained on existing IDs, and if they are unreliable, then the AI is unreliable: they should rather have retrained the AI on good data, and then re-evaluated it. This is the catch 22 with using CS data: you can only expect to get out what you put in: if you just grab the data, then expect it to be useless. But if you encourage observers, train them, provide them with guides and keys and advice, help with IDs and provide feedback, and vet and check the data, then it can be as good as can be. For lichens this means some lichen groups will only be good to family or genus or complex - but that is the way it works.

R. Troy McMullin and Jessica L. Allen (2022) An assessment of data accuracy and best practice recommendations for observations of lichens and other taxonomically difficult taxa on iNaturalist. Botany 100: 491–497 (2022) https://dx.doi.org/10.1139/cjb-2021-0160

Abstract
We assess the identification accuracy of ‘research grade’ observations of lichens posted on the online platform iNaturalist. Our results show that these observations are frequently misidentified or lack the necessary chemical and (or) microscopic information for accurate identification. Lichens are a taxonomically difficult group, but they are ubiquitous and eye-catching and are regularly the subject of observations posted on iNaturalist. Therefore, we provide best practice recommendations for posting lichen observations and commenting on observations. Data from iNaturalist are a valuable tool for understanding and managing biodiversity, particularly at this crucial time when large scale biodiversity decline is occurring globally. However, the data must be accurate for them to effectively support biodiversity conservation efforts. Our recommendations are also applicable to other taxonomically difficult taxa.

The recommendations are very good, but only for a lichen specialist. For your average naturalist or CS, these are way over the top. Basically these are guidelines developed by specialists for specialists, without any real regard for how to make it work for someone who is interested and wants to contribute, but does not want to carry a rucksack or take out a bank loan for some lichen observations. There is a need to develop some lichen-focussed CS, and for these the guidelines would be a most useful holy grail.
They also miss the point that downloading the data from GBIF should be the last step. First step is to go through the data and ID it, comment on it, and check it - this must be done on the source, so that the observations are improved., and a record of issues is provided. So GBIF might point you to the data, but the data needs to be checked and vetted and commented at source: i.e. on iNaturalist.

These recommendations are worth repeating, so I will add them as another journal article.

Thanks @beetledude for encouraging me to do this.

21,750 observations by 1,949 observers
35,025 identifications by 507 identifiers

3,610 observations (17%) to Research Grade
5,944 observations (27%) identified only as Lichens - help push them here
467 observations ((2%) identified to Order - help ID them here
2,874 observations (13%) identified to Family - help ID them here
7,904 observations (36%) identified to Genus - help confirm them here
1,002 observations (5%) identified to species level, but needing confirmation: - help confirm them here

265 "species"

Top Species ( more than 50 observations)

535 Xanthoria parietina Common Sunburst Lichen
405 Ramalina celastri Cartilage Lichen

281 Lasallia rubiginosa Red Toadskin Lichen
251 Crocodia aurata Gold Specklebelly Lichen
234 Teloschistes chrysophthalmus Golden-eye Lichen
230 Psora crenata Brick Scale

166 Cladonia confusa Fuzzy Reindeer Lichen
149 Xanthoparmelia hottentotta Cape Rock Shield
136 Genus Pertusaria - Pore Lichens
131 Teloschistes flavicans Golden Hair-Lichen
125 Teloschistes capensis Cape Hair Lichen
118 Flavoparmelia caperata Common Greenshield Lichen
107 Dufourea flammea Burning Finger Lichen
105 Lobaria pulmonaria Tree Lungwort Lichen

90 Flavoparmelia soredians Shadow Greenshield Lichen
81 Teloschistes pulvinaris Mat Hair Lichen
81 Complex Cladonia chlorophaea - Cladonia chlorophaea Aggregate
80 Genus Dirinaria - Dirinaria Lichens
80 Heterodermia leucomelos Elegant Fringe Lichen

72 Chrysothrix candelaris Powder Gold-dust Lichen
70 Teloschistes exilis Slender Orange-Bush
66 Cladonia floerkeana Gritty British Soldiers Lichen
65 Genus Haematomma - Bloodstain Lichens
62 Cladonia macilenta Lipstick Powderhorn
59 Dermatiscum thunbergii African Gold Lichen
51 Teloschistes puber Flathair Lichen
51 Dufourea turbinata Turban Lichen

Family Breakdown

6,435 Parmeliaceae - Shield Lichens and Allies
2,991 Teloschistaceae
1,017 Cladoniaceae - Spindles and Structured Lichens

929 Ramalinaceae
571 Ostropomycetidae
514 Lobariaceae
505 Physciaceae
408 Acarosporaceae
339 Umbilicariaceae
302 Psoraceae

256 Caliciaceae - Button and Allied Lichens
168 Collemataceae
162 Rhizocarpaceae
146 Chrysothricaceae
123 Roccellaceae

90 Lecanoraceae
65 Haematommataceae
54 Stereocaulaceae

25 Peltigeraceae
22 Arthoniaceae
21 Pannariaceae
16 Lecideaceae

7 Brigantiaeaceae
5 Fuscideaceae
4 Opegraphaceae
2 Nephromataceae
2 Sphaerophoraceae

1 Megalariaceae
1 Ophioparmaceae

Top Observers (more than 150 observations)

1 tonyrebelo 7,594
2 anthony369 1,301
3 nicky 827
4 gigilaidler 266
5 shauns 261
6 magdastlucia 241
7 vynbos 192
8 colin25 189
9 botaneek 186
10 dewald2 185
11 rosemary_harrison 180
12 ricky_taylor 162
13 botswanabugs 162
14 djwebster 155

Top Species Observers ( more than 15 species)

1 tonyrebelo 96
2 nicky 59
3 anthony369 45
4 botaneek 31
5 gigilaidler 23
6 magrietb 21
7 pietermier 20
8 sallyslak 20
9 christiners 18
10 yvettevanwijk1941 18
11 colin25 18
12 shauns 18
13 djwebster 17
14 tessabrunette 16

Top Identifiers (more than 100 identifications)

1 jurga_li 11,910 Many thanks: we would know nothing about our Lichens without your help!

2 tonyrebelo 1,581
3 ian_medeiros 772
4 dianastuder 612
5 vynbos 270
6 lotteryd 214
7 jeremygilmore 152
8 nicky 141

Determining the type locality and collector of Nylander’s South African lichens
Ian D. Medeiros 2019
Bothalia 49 https://doi.org/10.4102/abc.v49i1.2384

Abstract
Background: In 1868, Nylander described 15 new lichen taxa from collections made near Durban, South Africa. The locality was not specified and the collector was identified only as ‘Miss Armstrong’.
Objectives: To identify the collector and type locality of Nylander’s species.
Method: Scientific literature, maps, letters, notebooks and genealogical sources were consulted to reconstruct the provenance of the specimens.
Results: ‘Miss Armstrong’ was likely Olivia Armstrong; she collected in the Karkloof area of the KwaZulu-Natal Midlands.
Conclusion: This investigation facilitates future work to determine whether the species described and reported by Nylander are still extant in the same locality.

If you are aware of any other interesting lichen projects, please tell us:
(number = number of species Easter 2022 - 233 for this project)

Local:
92 https://www.inaturalist.org/projects/lichens-of-the-cape-peninsula
59 https://www.inaturalist.org/projects/lichens-of-the-namib-desert

Med Regions:
41 https://www.inaturalist.org/projects/north-african-lichens
843 https://www.inaturalist.org/projects/lichens-of-california
(California fog: https://www.inaturalist.org/projects/lichenicolous-fungi-of-the-world (why trad?))
(s Cal: https://www.inaturalist.org/projects/lichens-of-southern-california (why trad?))

Global:
1323 https://www.inaturalist.org/projects/lichens-of-europe
3734 https://www.inaturalist.org/projects/lichens-of-the-world
3782 https://www.inaturalist.org/projects/world-s-lichens
(https://www.inaturalist.org/projects/earth-s-lichens (why trad?))

by Country:
165 - https://www.inaturalist.org/projects/lichens-of-mongolia
231 https://www.inaturalist.org/projects/lichens-of-finland
281 https://www.inaturalist.org/projects/lichens-of-italy

322 https://www.inaturalist.org/projects/lichens-of-ukraine
363 https://www.inaturalist.org/projects/australian-lichens
410 https://www.inaturalist.org/projects/lichens-uk

606 https://www.inaturalist.org/projects/lichens-of-germany
940 https://www.inaturalist.org/projects/lichens-of-nz
(https://www.inaturalist.org/projects/crustose-lichens-of-new-zealand)
1032 https://www.inaturalist.org/projects/lichens-of-eastern-united-states (why trad?)

fungi that live off lichens (i.e. Lichen fungal parasites):
239 https://www.inaturalist.org/projects/lichenicolous-fungi-of-the-world

for fun: it cannot be serious -

https://www.inaturalist.org/guides/10634?view=card

The Lichen species of South Africa as per
Alan M. Fryday 2015. A new checklist of lichenised, lichenicolous and allied fungi reported from South Africa Bothalia; Vol 45. doi: 10.4102/abc.v45i1.148
has been added to https://www.inaturalist.org/check_lists/1666357-Lichens-of-South-Africa

The current list includes 1750 taxa in 260 genera from mainland South Africa, with an additional 100 species and 23 genera from the sub-Antarctic Prince Edward Islands, which are treated separately. ... It is estimated that, when fully explored, the lichen biota of South Africa will consist of somewhere between 2500 and 3000 taxa.

The following species not found in dictionary and thus not added:
Amandinea natalensis
Anaptychia obesa
Bacidia subluteola
Bactrospora africana
Blastenia imponens, Blastenia psorothecioides, Blastenia punicae, Blastenia sedutrix
Buellia discolorella, Buellia italica (=Buellia spuria), Buellia protothallia
Caloplaca ferrogineovirens, Caloplaca hampeana, Caloplaca subcerina, Caloplaca sympageella, Caloplaca subsoluta, Caloplaca phlogina
Canoparmelia crozalsiana
Collema coccophorum, Collema crispum, Collema polycarpon, Collema tenax
Diploschistes diacapis
Echinoplaca strigulacea
Graphina bylii
Gyalideopsis athallinoides
Heppia guepini
Heteroderma diademata, Heterodermai microphylla, Hetreodermia obscurata, Heterodemia spathulifera, Hetrodermia tremulans
Lasallia capensis, Lasallia dilacerata
Lecanora thiocheila, Lecanora vanderbylii
Lecidea aeneola, Lecidea geina, Lecidea squamifera
Lopadium woodii
Megalospora stellenboschiana, Megalospora tuberculosa
Nephroma tropicum (=Nephroma helveticum)
Ochrolechia capensis
Parmotrema natalensis
Peltigera sorediifera
Pertusaria wawreanoides
Phaeophyscia adiostola
Physcia tribacea
Placidium kaernefeltii
Pleurotrema trichosporum
Pterygiopsis melanophthalma
Ramalina lanceolata
Rinodina confragulosa
Siphula dregei, Siphula flavofvirens, Siphula incrustans
Sporopodium xanthleucum
Sterocaulon delisei, Sterocaulon esterhuyseniae
Sticta hornemanni
Tapellaria epiphlla
Usnea flaccidoangulata, Usnea gonioides
Xanthoparmelia brevilobulata, Xanthoparmelia disitifolia, Xanthoparmelia exornata
Xanthoparmelia ganymedea, Xanthoparmelia leptoplaca, Xanthoparmelia lyrigera
Xanthoparmelia microscopica, Xanthoparmelia mucinae, Xanthoparmelia perspersa, Xanthoparmelia perspersa
Xanthoparmelia salazinica, Xanthoparmelia schenkiana, Xanthoparmelia subchalybaeizans, Xanthoparmelia vernicosa
Xanthoria dissectula
Zwackhia bonplandii

High Altitude Lichens

From http://nhm2.uio.no/botanisk/lav/RLL/PDF1/R456.pdf
Lichens at high altitudes in Southern Africa O. Almborn 1987
Abstract:
It is still premature to present a detailed survey of the lichen biogeography of southern Africa but some patterns may be distinguished. The montane species (more or less corresponding to the alpine species of the Northern Hemisphere) form a fairly large group. They occur mainly at high altitudes; usually about 1000 m and are saxicolous or terricolous. A number of the montane species are endemics. Others also occur in the central African mountains. Species known from high mountains in southern Africa and also from southern America or Australia/New Zealand are of special interest to the phytogeographer; and may be relicts from the ancient Gondwana
This deals with the species listed below; with maps.

Some key points:
South Africa has a few cosmopolitan lichen species; for instance;

• Candelaria concolor * Lobaria pulmonaria * Peltigera canina * Xanthoria parietina On the other hand; many species well known from the Northern Hemisphere are absent:
  Cetraria islandica; Cladina rangiferina; Evernia prunastri; Pseudevernia furfuracee; Parmelia saxatilis and Parmelia sulcata
  There are also many endemic species; such as

• Combea mollusca * Roccella hypomecha * Roccellina capensis (Dirina capensis)
• Teloschistes capensis * Xanthodactylon flammeum (Xanthoria flammeum)

• Xanthomaculina hottentotta (Omphalodium hottentotta Or Parmelia hottentotta)
  It must be emphasized; however; that the lichens; like other groups of cryptogams; have few equivalents to the high number of endemic families; genera and species known from the phanerogamic flora.
  Species mentioned are posted here:

Note posted: Lasallia capensis, Lasallia dilacerata, oelocaulon epiphorellum