Transcript An introduction to the diversity of animal life

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.
Species
The 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 fossils
A 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 Diversity
Then 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.
LUCA
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
Eubacteria Archebacteria
Eukaryota
plants
protists fungi
animals
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
Sp3
Genus 1
Genus 2
Genus 2
Sp2
Sp4
Genus 1
Genus 2
Genus 1
Sp5
Genus 1
Genus 1
Genus 1
Sp6
Genus 1
Genus 1
Genus 1
Sp7
Genus 1
Genus 1
Genus 1
Note that there is now a problem with
polyphyly – genus 1 is polyphyletic, does
not have 1 unique common ancestor.
Is OK
Is not OK
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
Squamata
lizards snakes
dinosaurs
tuatara
archosaurs
crocodiles birds
mammals
tuatara
If birds are not
reptiles, then
‘reptiles’ is not a
valid clade as there
is no unique
common ancestor
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 teasers
Recent 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 Termites
Termites
cockroaches cockroaches
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 resplit).
Leucojum
Galanthus
Was Leucojum, is Acis
Taxonomic hierarchies
These 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:
Eukaryotes:
Nb ‘Protists’
Animals
is
Plants
polyphyletic.
Fungi
protists
Prokaryotes
Eubacteria
Archaebacteria
(Viruses would count as a 7th, if
you regard them as alive).
The Synthetic Kingdom
A 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
Blue tit
Parus caeruleus Cyanistes
caeruleus
Common
lizard
Fruit fly
Natterjack
Toad
NOW!
Lacerta vivipara Vivipara vivipara
Drosophila
melanogaster
Sophophora
melanogaster
Bufo calamita
Epidalea
calamita
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
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.
Pan/Homo
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
Genome
Junk DNA – no selection
pressure, varies quasirandomly between
individuals
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 hierarchy
Eukaryota:
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”.
1st name has a capital letter, 2nd does not
Homo sapiens
OR Homo sapiens
On a PC make the font italic
When writing by hand
underline the name.
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)
Sminthurus
Adenia
(passifloracea)
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)
Pronunciation
There 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.
Dicyrtoma
Dick – row – tomer? Dye – sir – tomer?
So I put out a global
email asking how to
say this:
Dee-zeer-to-mah
Dee – churr – tome –er
Dye – sir – tomer – a
[A as in “jam”]
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 saccharina
Now 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.