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- Geography, Morphology, and Genetics

There has been a fascinating discussion of phylogenetics in the on-line discussion group of the Pacific Bulb Society the past several days. I've not been able to resist getting involved, even though my professional expertise does not include taxonomy or phylogenetics, and not even DNA sequencing. I'll try to reproduce the ideas raised by several participants here, but in a very general way.

Geography's Relation to Species

Every botanist and zoologist knows that the single most important piece of data that must accompany every specimen collected is its precise geographical location when collected. Date when collected is also important and very helpful. The name of the collector is usually included in the collection data. But the "where" is the sine qua non for biological specimens collected in the wild.

In our discussion of the possible identity of a bulb specimen one of the members had received, we felt that the missing collection locality would have been of critical importance in providing an identification. While this seems self-evident to me, it was apparently not seen that way by all the participants in the discussion. What is the importance of geography, and why is it questionable?

Locality is important, of course, because it confirms and potentially extends the known habitat range of the species. It is of uncertain value in determining what species one has collected, since species may grow wild outside their known range, or other species ranges may overlap a given species' range.

Where locality data is helpful in determining species identities is where the known species resemble each other closely in physical appearance but are known to have discrete and separate geographical ranges. Since this is not all that rare a circumstance in biology, knowing the collection locality for an ambiguous specimen can tell you its identity.

Still, I see geography as two levels removed from the actual identity of a specimen.

Morphology's Relation to Species

Traditionally, morphology, the physical structure of the organism, was the sole basis for classification. We identified species by the physical characteristics of the plant or animal, and inferred relationships strictly on the basis of these. Used this way, morphology will give you answers that are determined by the limitations of the kinds of data you utilize. Morphology is actually one level removed from phylogenetic relationship. It does not actually address genetic relatedness, as far as I can tell, although it was the traditional basis for all phylogenetics.

Since morphology is comprised of the results of genotype interacting with environment, a given species may have a variable morphology depending on climate, geography, and human alterations to its environment. Then too, different species may converge in physical appearance in response to living in a similar or the identical environment and habitat. Questions of structural convergence in response of similar evolutionary pressures seem to me to require molecular genetic analyses for clarification. I am reminded of the phenomenon of "cryptic sibling species" in butterflies, but those were first uncovered by detailed morphological studies (of the male genitalia, as I recall), prompted by observed behavioral differences. They nonetheless still pose an epistemological question.

Morphology was our first and original tool for studying phylogenetics and, if I'm not mistaken, the sole basis until DNA sequencing was invented; but it can also mislead.

When DNA sequencing came along, it opened a new and entirely different window on what constituted a species.

Species Definitions and DNA

We have reached the point in modern biology where one can say that the DNA sequence IS the organism. The genome defines the organism. It would follow from this then that the species is definable from DNA sequence data as well. Since we know that sexually-reproducing organisms almost never have two individuals who are precisely identical in the DNA sequences, we will have to learn to define the sequence variation that a given species concept can include.

How one defines "species" is dependent on what one intends to use the definition for. Look in many books on phylogenetics and you will see several formal definitions of species. Biologists use different ones of those several definitions depending on what direction their research is taking and what methodologies are available to them to use.

The one I think is most popular, the concept of the Biological Species as the interbreeding population, is fraught with problems. Operationally, the weakness in the biological species concept is that we can rarely if ever actually define the "breeding population." It is not really definable (in terms of "do this then this and you define the breeding population") using any doable steps so it is not really a scientific concept.

This leads me to feel that there is probably no such thing as a "species" but rather many ways of viewing the biological world. That is, it seems clear that there is not at present a single unambiguous working definition for the concept. I infer from this that the concept we are trying to define may in fact not exist as a single logical entity. Our discomfort with this, if any, is probably because our subconscious minds are still trying to fit everything into a pre-Darwinian frame of reference, which contained fixed, rigid species. Taxonomy needs to be viewed not as the Platonic Ideal of biology but rather as a heuristic tool for use in real life.

I think that a future definition(s) of "species" will attempt to circumscribe the "envelope" of DNA sequences that are encompassed by a given species. This answer will probably be different for different species. I think it will be very different for plants than for animals; and microbiologists seem to have already gone off on their own very separate track for defining populations rather than species. Binomial nomenclature seems to be giving way to serial numbers that computers can more easily handle. You don't draw pictures of phylogenetic trees, you calculate new ones using the latest data as you need them. Today's tree won't look like yesterday's unless the databases were locked down overnight.

An excellent reference for the nature of species is "Speciation" by Jerry A. Coyne and H. Allen Orr, available from amazon.com, as of this writing. Pub. 2004 by Sinauer Associates, Sunderland, MA.

These comments contain direct quotes from my personal posts to the on-line discussion group of the Pacific Bulb Society on October 31, 2012, with minor changes in wording.

Impending Travel

We will be traveling to Tanzania for a tour of Tarangire, Ngorongoro, Serengeti, and Olduvai. I don't know how to post new entries to this blog using the iPad we are carrying with us, so I will post some pictures during the trip to my facebook page, ShieldsGardens on Facebook.com. After we return home, I'll try to post more pictures and a summary of the trip to this blog. I think this is the dry season in Tanzania, so I don't really expect to see many plants. We're going in order to see the animals!

Good gardening, from here in central Indiana


Look up technical terms in the Glossary of Plant Biology

- Safari in Tanzania. I. Plants

We have returned from our tourist safari in Tanzania. Tanzania lies just to the south of the Equator, so there are no particular summer or winter seasons. January was said to be the hottest month of the year. While there are lots of pictures of wild animals to share, there are also a very few pictures of flowers as well. I'll start with the flowers.

There are two rainy seasons in Tanzania, a small one in November, December, and January, which is fed by convection from the large freshwater lakes bordering Tanzania to the west: Lake Victoria and Lake Tanganyika. There is also a big rainy season, fed by the monsoons in March, April, and May, coming in off the Indian Ocean which bounds Tanzania on the east. There had been some light rain about two weeks before we arrived, representing an earlier-than-usual start to the small rainy season. As a result, the countryside was greening up, and we had the good fortune to see a few bulbs in bloom.


Ammocharis tinneana occurs in East Africa, including Tanzania. It looks very much like A. coranica from South Africa, and from a distance is easily confused with it. We saw only a few of these, usually not in any sort of group.

Ammocharis tinneana in Tanzania (c) copyright 2012 by James E. Shields.  All rights reserved
Ammocharis tinneana in Tanzania

None were in seed, and several plants were still just flower buds, like the one shown above.


We saw many plants that were clearly Crinum macowanii. They tended to grow in moist areas but not right down in the wet areas. We saw this species in Tarangire National Park, in the Ngorongoro crater at about 6000 ft. el., and even in a couple places in the Serengeti.

Crinum macowanii in Tanzania (c) copyright 2012 by James E. Shields.  All rights reserved.
Crinum macowanii in habitat in Ngorongoro, Tanzania

Crinum macowanii (c) copyright 2012 by James E. Shields.  All rights reserved.
Crinum macowanii in Tanzania

There was another species of Crinum at one location. The peduncle (stem) was only a couple inches tall when we were there, and the umbel bore only one or occasionally two flowers. The flowers looked white from a distance, and the local vernacular name for them was "Waste Paper." Close-up, the petals had a faint pink midrib band on the outside. They grew as a scattered colony in an area that showed signs of having recenly been covered by run-off from a rainfall. We only saw them in one single location.

Crinum species in Tarangire (c) copyright 2012 by James E. Shields.  All rights reserved.
Crinum sp. indeterminate, in Tanzania

The leaves were very narrow and strongly channeled or canaliculate. The foliage seemed to be just getting started growing, so I am not sure what the mature leaves might look like.


We saw occasional isolated blooms of a Scadoxus species that most probably was Scadoxus multiflorus multiflorus, from the Lodge at 7500 ft. el. on the Rim of the Ngorongoro crater to a Kopje in the Serengeti at about 4000 ft. el. The colors varied from very bright orange to a deep rich red.

Scadoxus multiflorus multiflorus in Tarangire (c) copyright 2012 by James E. Shields.  All rights reserved.
Scadoxus sp., cf. multiflorus subsp. multiflorus

There are only a limited number of species of Scadoxus, and only multiflorus ssp. multiflorus seems to extend its range through Tanzania. This one puts up its scapes before the leaves appear, which is consistent with the descriptions of multiflorus multiflorus.

Good gardening, from here in central Indiana


Look up technical terms in the Glossary of Plant Biology

- Safari in Tanzania. II. Plants and Animals

Mystery Crinum Species

The unknown Crinum species appears to be one of a small group of possible species:

  • Crinum acaule (Namibia, South Africa)
  • Crinum minimum (Tanzania, Zambia)
  • Crinum piliferum (Kenya)
  • Crinum walteri (Namibia, South Africa, Zimbabwe)
This is according to Dr. David Lehmiller, who has studied Crinum of Southern Africa and Madagascar extensively. The ranges of none of these species are known with absolute certainty. The distinctions lie mainly in the structure of the fruits and of the seeds. We can't say for sure what we saw in Tanzania based only on my photographs. The betting, depending on whom you talk to, is either on C. minimum or on C. walteri.

Checklist of Amaryllidaceae of Tanzania

An advanced search of the Kew online web site for "Amaryllidaceae" and "Tanzania" gave the following list of species.

  • Ammocharis angolensis (Baker) Milne-Redh. & Schweick.
  • Ammocharis tinneana (Kotschy & Peyr.) Milne-Redh. & Schweick.
  • Boophone disticha (L.f.) Herb.
  • Brunsvigia kirkii Baker, Handb. Amaryll.: 99 (1888).
  • Crinum kirkii Baker
  • Crinum macowanii Baker
  • Crinum minimum Milne-Redh.
  • Crinum ornatum (Aiton) Herb.
  • Crinum papillosum Nordal
  • Crinum politifolium R.Wahlstr.
  • Crinum stuhlmannii Baker subsp. stuhlmannii
  • Crinum subcernuum Baker
  • Cryptostephanus haemanthoides Pax
  • Cyrtanthus breviflorus Harv.
  • Cyrtanthus sanguineus (Lindl.) Walp.
    • Cyrtanthus sanguineus subsp. minor Nordal
    • Cyrtanthus sanguineus subsp. wakefieldii (Sealy)
  • Nothoscordum gracile (Aiton) Stearn
  • Pancratium tenuifolium Hochst. ex A.Rich.
  • Scadoxus multiflorus (Martyn) Raf. subsp. multiflorus Scadoxus puniceus (L.) Friis & Nordal
  • Tulbaghia cameronii Baker
  • Tulbaghia rhodesica R.E.Fr.
  • Tulbaghia violacea Harv. subsp. violacea

We saw an Ammocharis, which I presume to have been A. tinneana, but at this point I still don't actually know what distinguishes A. angolensis from A. tinneana.

Elephants of Tarangire

The characteristic animals of Tarangire are the elephants, which find refuge there in the dry season. Elephants need a lot of water, and the Tarangire river never dries up. The elephants can't stay there all year, because the soil is deficient in phosphate, which pregnant and lactating mothers need. So when there is sufficient moisture elsewhere, the elephants leave Tarangire to browse where there is more phosphate in the soil and hence in the plants they eat.

Elephants in Tarangire (c) copyright 2012 by James E. Shields.  All rights reserved.
Elephants in Tarangire

The elephants come and go from Tarangire with no warning. Two days before we arrived, there were no elephnats in Tarnagire National Park. Two days after we left, there was again not a single elephant in the park. While we were there, one could see literally a hundred elephants at a time in the Tarangire river valley.

Elephant mother and calf in Tarangire (c) copyright 2012 by James E. Shields.  All rights reserved.
Elephants in Tarangire

If all the elephants that gather seasonally in Tarangire stayed there all year long, they would eventually overwhelm the ecosystem. They need to leave, not just to obtain sufficient phosphate in their diets but to preserve the Tarangire river valley for future generations of elephants to use in times of need. I wonder if they realize that?

Elephant playing in a mud hole (c) copyright 2012 by James E. Shields.  All rights reserved.
Elephants in Mud

Finally, some adult elephants trying to get babies and calves to stop playing in a mud hole and let the herd move on. The adults looked very human, and frustrated, trying to deal with slippery, happy, squirming babies having a really great time! It seems you can't just grab a playful baby elephant by the ear and drag her out of the mud.

Good gardening, from here in central Indiana


Look up technical terms in the Glossary of Plant Biology

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Last revised on: 27 November 2012
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