Biodiversity and taxonomy

Peter Shaw

RU“From the first dawn of life, all organic beings are found to resemble each other in descending degrees, so they can be classed in groups under groups.”

Charles Darwin, Origin of Species, Chapter 13

Structure of the lecture:

Title: Biodiversity and taxonomy

Contents:

Biodiversity

what, where

Taxonomy:

how done, jargon used.

I aim to introduce you to the range of life on the planet and how we classify this huge diversity.

This framework has a natural hierarchical structure (meaning it can be shown as a dendrogram) – giving us biodiversity, which is

studied and described by the science of taxonomy.

Dendrogram Taxonomy – the study of the classification of life forms.

SpeciesThe core of classification is the notion of a species. For large, complex things like animals the test is easy; can a male of one population produce a viable, fertile embryo with a female? If no differences show, 2 populations that never mix can still be the same species, eg azure winged magpies (only in Portugal and E China!!).Usually species are defined by morphology, though DNA separation is increasingly useful for this.

With plants, hybrids are commoner, but chromosome number is stable, so often botanists squash tips to count chromosomes (and hence identify the parents).

With microbial groups, there is no true sexual exchange, but extensive gene swapping that rather undermine the tree structure we like to impose.

Patterns in biodiversity:

• The clearest pattern is with respect to size. There are many more species of small organisms than of large ones. Roughly 10* smaller = 10* more species.

• The distribution of species numbers is very irregular between life forms – mammals are one of the most minor of groups!

Beetles

• JBS Haldane was once asked what zoology revealed about the mind of God.

• “An inordinate fondness for beetles” he replied. Beetles are the most species-rich group on the planet (though bacteria could probably beat them if we could only isolate them all).

Mind-numbing figures.

• Work in the 1990s fogged insects out of 19 individuals of 1 tree species in Panama. They found 682 species of herbivores, 296 of predators, 69 of fungivores and 96 scavengers.

• A few assumptions allow these figures to give you an estimate of 30 million spp. in total – just insects, in tropical trees.

• Current thinking is that this is rather high, and that the true total is closer to 10 million. We will never actually know :=(

Ancient biodiversity

A few species deserve honourable note for their persistence, barely changed over geological eras. Many coniferous trees have changed little since the Triassic, notably Ginko (maidenhair tree) and many cycads.

Marine living fossilsA few life forms have changed little or not at all since the dawn of animal life. These mainly inhabit the ocean depths, and include the crinoids which once filled carboniferous seas, and Latimeria – the coelocanths that dominated the Devonian seas.

The prize for least changed goes to an obscure inarticulate brachiopod called Lingula, which has fossils looking like modern forms back in the Devonian, and was a main survivor in the anaerobic oceans of the permo-triassic MEE.

DNA DiversityThen in the 1990s DNA technology allowed scientists to probe the diversity of life in new ways. The evidence is overwhelming that we are surrounded by immense levels of genetic diversity that is invisible to us as the microbes will not culture. Say 1000 new sp in a gram of soil – typical initial values.

A DNA sequence in seawater turned out to be the commonest organisms on the planet, a hitherto unknown microbe called Pelagibacter ubique.

So how many species?

Our persistent ignorance of basic global biology is a matter for concern. We have c. 2E6 spp named, and think that there may be c. 10E6 species. Other figures have put it higher, up to 30E6, but we will never know. To a first approximation all animals are tropical beetles, but even their diversity is dwarfed by the genetic diversity among soil microbes.

Say 10 million species, and several thousand new to science in each pinch of soil.

Is there just 1 correct taxonomy?

Of course, many ways to classify life forms, some obviously trivial (colour), others less so (symmetry or embryology). Yet old classifications are routinely changed – mass changes in the face of DNA evidence (more soon). Before the details of DNA taxonomy, the philosophy. How can there be one absolute correct model?

It comes straight out of the evolutionary paradigm; go back far enough and any 2 species will be linked by a common ancestral population. This fact allows you to draw dendrograms (usually dichotomous), giving a natural structure to the classification. If your system of names gives a different structure, you must change it.

The evidence of modern life forms is clear; all extant life forms came from one ancestral design. LUCA - the Last Universal Common Ancestor. One system bundled itself into phospholipid bubbles and coded itself its amino acids on DNA with an arbitrary mapping, that has permeated all subsequent life.

LUCA

LUCA

Eubacteria Archebacteria

Eukaryota

animalsfungiprotistsplants

Clades

A clade is a term referring to the group comprising an ancestral species and all its descendant lines. The group MUST be monophyletic (one unique common ancestor). Thus all humans are a clade (common ancestor <140 KYBP), nested inside the larger clade of all mammals.

The scary-sounding school of cladistics merely tries to allocate organisms to clades – to hammer out their family trees.

Ancestral popn.

Sp1 Sp2

Sp3 Sp4 Sp5 Sp6 Sp7

Genus 1 Genus 1 Genus 1 Genus 1 Genus 1Genus 2 Genus 2 Genus 1 Genus 1 Genus 1Genus 2 Genus 1 Genus 1 Genus 1 Genus 1

Is OKIs not OK

Genus 2 Genus 2 Genus 1 Genus 1

Note that there is now a problem with polyphyly – genus 1 is polyphyletic, does not have 1 unique common ancestor.

Beware false clades!There is a recurring mis-match between evidence-based cladistics and human-based common sense. It was first exemplified by the false clade “reptiles”, but recent DNA work has thrown up many similar cases.

Reptiles: anaspids, diaspids, (synapsids)

Turtles etc

lizards snakes dinosaurs tuatara

mammals

Squamata archosaurs tuatara

If birds are not reptiles, then ‘reptiles’ is not a valid clade as there is no unique common ancestorcrocodiles birds

In simple English; from the viewpoint of evolutionary history, the closest relatives of crocodiles are birds, not lizards. Forget common sense – 100 MY evolution can give an utter transformation. “Reptile” is a valid GRADE but not a CLADE.

(We knew this before DNA, from Cretaceous fossils)

Similarly, the closest land cousin to an elephant is the hyrax. (Again Victorians knew this from the foot and jaw anatomy). Dugongs turn out to be a bit closer still to elephants.

More recent teasersRecent DNA work allows us to see past the problem that, just sometimes when a new adaptive window opens, rapid evolution occurs in body parts that hides true relationships.

Cockroaches, insect order blattodea, go back to the carboniferous.

And in the Jurassic (?), some wood eating cockroaches because eusocial. These early termites became very successful, the order isoptera.

Cockroaches cockroaches cockroaches cockroaches

Cockroaches cockroaches cockroaches cockroachesTermites

Termites

Termites

termites

Hence we cannot keep termites and cockroaches as equal status orders. Probably termites will become a family within blattodea.

One more example; gardeners have long cherished Galanthus, the snowdrops.

Recent molecular work shows Galanthus to derive from within the wider genus Leucojum (the snowflakes). The obvious solution is to lose the genus Galanthus, but the name is so popular that instead the genus Leucojum was split into 2, with a new genus Acis being created (or rather, the 1807 genus that had been merged has been re-split).

Leucojum Galanthus Was Leucojum, is Acis

Taxonomic hierarchiesThese are about seeking common features unifying all the organisms in a named group. The deepest split of all is between two ways of organising cells – the eukaryotic cell (with a nucleus and organelles) and prokaryotic cells (with DNA loops floating free in the cytoplasm). The 6 kingdom system (Woese et al) gives us:

ProkaryotesEubacteriaArchaebacteria(Viruses would count as a 7th, if you regard them as alive).

Eukaryotes:AnimalsPlantsFungiprotists

Nb ‘Protists’ is polyphyletic.

The Synthetic KingdomA Natural History of the Synthetic Future

Tree of life project – check out the website

See

http://tolweb.org/ ToL avoids naming levels like phylum.

http://botit.botany.wisc.edu/courses/systematics/Phyla/Phylum_directory.html

Name changes

The downside of new taxonomic techniques is that old names get lost.

English name

familiar scientific name NOW!

Blue tit Parus caeruleus Cyanistes caeruleus

Natterjack Toad Bufo calamita

Epidalea calamita

Fruit fly Drosophila melanogaster

Sophophora melanogaster

Common lizard Lacerta vivipara

Vivipara vivipara

Where do we fit in?It is a good exercise to ask yourself where you fit in.. (Read Dawkins’ “The Ancestor’s tale”)

A useful model is to ask yourself about your ancestors. After a while it’s not so much about individuals as populations; if there is a link to one member of an ancestral group, eventually (c. 25 generations) all members have equal claim to being your ancestor, along some gene line.

Some gene lines we value highly because they don’t exchange; the Y chromosome for men, the mitochondrial line for women.

Go back to the common ancestor of Y lines. For a while we thought that this sequence started diverging c. 65,000 KYBP. (About 10kyrs after the time of Toba blowing 74 KYBP, and about the time we started wearing clothes, according to DNA divergence in head and body lice.) Recent work added African pygmies and redated to 140KYBP (Cruciani et al 2011).

you humanity Chimps Bonobos

Pan/Homo

The same question for women gives us a mitochondrial Eve c. 190,000 KYBP, roughly as old as mankind.

Line up with your father (or his shade) behind you, and his father before that, and keep going backwards. 1.5 km back all humanity shares the same line. A chimpanzee beside you does the same, and about 60km back you find the 2 queues join. Chimpanzees are our closest cousins, and we are theirs.

We meet up with other old world monkeys in the oligocene, c. 25 MYBP.

Lemurs and bushbabies split off c. 63MYBP

Rodents split off c. 75 MYBP.

Afrotheres – elephants, aardvarks, elephant shrews, left our tree c. 105 MYBP. Our ancestor then looked like a large shrew.

Birds and reptiles join up c. 300 MYBP – your family would have been lizard-like then.

Going back much further (>1000,000,000 years if you believe the DNA evolution rate estimates) we had a common ancestor with starfish, or rather crinoids (as these actually came along first.) The victorians knew this – there is a key quirk of embryonic development that unites chordates and echinoderms.

Another 3BY earlier came LUCA.

DNA-derived phylogenies

Junk DNA – no selection pressure, varies quasi-randomly between individuals

Genome

Useful genes – can’t vary greatly within 1 species

Active site of crucial enzyme – changes hardly ever happen

An example of a crucial sequence that changes very slowly and may be used to derive high-level taxonomic relationships: the ribosome has to bid exactly to mRNA and to all the tRNAs or the organism will die before its first cell division. rRNA homologies are used to establish relationships between phyla.

The taxonomic hierarchyEukaryota:Kingdom - Animalia

Phylum - Arthropoda

Class - Insecta

Order - Collembola

Family - Entomobryidae

Genus Entomobrya

Species Entomobrya nivalis

 Species - the basis of taxonomy, dignified by a Latinised binomial = the scientific name: Homo sapiens, Apodemus sylvaticus, Lumbricus terrestris. (I dislike the term “latin name”, since it is not Latin but merely latinised. Others find it acceptable, but I would encourage ‘Scientific name’)

How to write a scientific name!So many students get this wrong that I want to tell you now, at the start of your careers, how to write these names. Remember that getting it wrong is equivalent to saying “I have not been formally trained in biology”.

Homo sapiens OR Homo sapiens

When writing by hand underline the name.

1st name has a capital letter, 2nd does not

On a PC make the font italic

1 Phylum – many Phyla

The concept of a ‘phylum’ was developed in one kingdom, the animals. Luckily there are few hidden catches here – it is usually pretty obvious if a life form is an animal or not, though at the single celled level things can get rather blurred. (Volvox is a single celled green, photosynthetic entity which can ingest particulate food. It has good claims to be both animal and plant).

The next level down from kingdom is the one that REALLY matters for classifying animals. It is called Phylum, plural phyla.(NOT fila, as a student once wrote in a failed exam paper…)

There are about 30 animal phyla, each with a deep underlying similarity of body form. Once you can place an animal in its phylum you have made an excellent start towards understanding its anatomy.

In the interests of conformity, other kingdoms have taken to use the phylum-class-order hierarchy, although you won’t find it in the older botany textbooks (although they are otherwise excellent).

There is one oddity about naming that puzzled me when I first met it. The names must be unambiguous (eg no-one can create a new genus of animal called Homo, or a plant called Poa, as these genera exist. Nor can one create a new species with the same name as a pre-existing one, though sometimes new names are so irritatingly close that you feel like yelling at someone.

My pet dislike are the herbs Mignonette and weld, both in the genus Reseda. Weld is R. luteola, and mignonette is R. lutea. I always have to look it up…

Genus names can be almost identical too:

Adenium (apocyanacea)

Adenia

(passifloracea)

Sminthurus Sminthurinus Sminthurides

Shared names across kingdoms

But you can have the same name for an animal and a plant. The first time I met it was the genus Oenanthe – toxic plants, and a genus of birds called Wheatears..

Oenanthe crocata

Oenanthe oenanthe

Silly but true scientific names

• Ba humbugi Solem, 1976 (a snail from Mba Island, Fiji)

• Aha ha Menke, 1977 (an Australian sphecid wasp; and also Menke's car license plate number!)Agra vation Erwin, 1983 (a carabid beetle)Zyzzyx Pate, 1937 (a wasp)

• Pison eu Menke, 1988 (a South American wasp)

Ia io Thomas, 1902 (chinese bat; the shortest binomial, probably the only all-vowel binomial)

Gammaracanthuskytodermogammarus loricatobaicalensis Dybowski, 1926 (amphipod; the longest binomial)

PronunciationThere are no agreed standards for pronunciation! I’ve heard an US citizen talk about Sye-loss-obby for what I call Sigh-Low-sigh-bee.

DicyrtomaDye – sir – tomer?Dick – row – tomer?

So I put out a global email asking how to say this:

Dee – churr – tome –er

Dye – sir – tomer – a

[A as in “jam”]

Dee-zeer-to-mah

Precedence

The rule of precedence states that if two publications both describe the same species (as often happens) the first publication takes precedence. Even if everyone likes the old name! You can split a genus for reasons based on evidence – morphology or DNA.

There are legalistic touches, eg if the publication is undated its date defaults to 31-12 of its year, so loses precedence to a paper in a journal that does give the date!

Lepisma was named by Carl von Linne himself:

Lepisma saccharinaNow L. saccharinum

Lepisma comes from greek for a scale, which is gender neuter in latin. Linne used it as a feminine word, hence L. saccharina. There was then a motion passed in 1955 to redesignate the genus Lepisma as feminine not neuter. This meant its containing family had to be Lepismatidae not Lepismidae (!). There was mixed practice with the derived genera such as Ctenolepisma, some taken as feminine, some as neutral.

I think that the next proposal (due 2011) will define Lepisma as neuter, so it’s now Lepisma saccharinum. Showing that Linnaeus made a grammatical slip.