Download Why Do Names Keep Changing

Why Do Names Keep
Changing
- an explanation of many recent
classification changes
Presented by
Terry Moore
Definition of a New Species
Classically by morphological differences.
During the last century protein sequences added.
Most recently, RNA and DNA sequencing is causing a
change of attitude which now veers towards an
evolutionary approach.
“Our classifications will come to be, as far as they
can be made so, genealogies”
(Charles Darwin from the Origin of |Species)
Classification Definitions
Taxonomy – Study of taxons or groups which share
certain characteristics.
Phylogeny or phylogenetic systematics – a classification
which tries to reproduce evolutionary relationships.
Cladistics – an approach to classification in which
organisms are grouped (clades or cladograms) according
to whether they share characteristics with their
evolutionary ancestors.
Certain Problems Arise with ALL Approaches
Homoplasy – characteristics evolve in parallel &
convergently e.g.
echolocation in bats & whales. Both need high
frequency audio-sensitivity.
multiple plant origins of C4 photosynthesis
Horizontal transfer – especially through plasmids.
Epigenetics – through DNA methylation and
phosphorylation
Explanation of
DNA – deoxyribonucleic acid (double stranded) &
RNA – ribonucleic acid (normally single
stranded)
(Rasmol script used. If you have or want to have the
Rasmol program please contact Terry Moore)
How Do Cells Use DNA & RNA
1: Cells function via proteins for structure and enzymes
(protein catalysts).
Proteins are strings of amino acids.
There are 24 amino acids coded by DNA plus a start
and stop signal (total 26) and 4 different types of base.
1 base / codon codes for 4 amino acids
2 bases / codon codes for 16 amino acids
3 bases / codon codes for 64 amino acids
Enough! This is the called the triplet code but there is
redundancy.
Redundancy
How Do Cells Use DNA & RNA
2: Making RNA – Transcription
RNA types are: ribosomal RNA (rRNA) ,
messenger RNA (mRNA),
transfer RNA (tRNA)
rRNA composed of a :
large subunit (60S composed of 28S, 5.8S, 5S subunits)
&
small subunit (40S composed of 18S subunits)
How Do Cells Use DNA & RNA
3: Making protein – Translation
Video- double click to see
How Do Cells Use DNA & RNA
3: Making protein – Translation
4: Replication – each time a cell divides it has to separate
and make a new copy – a dangerous time.
Each cell has ~2m DNA when stretched out
Human on average has 1013 cells or 2x1013m DNA
Introns
- An intron is any nucleotide sequence within a gene
between exons that maybe removed and is not often
expressed in a protein.
- Humans average 8.4 introns / gene
- Most excised at mRNA stage but some are left
depending on the type of cell or the time
Where are DNA & RNA found
RNA is located in the
cytoplasm of the cell,
the mitochondria and
certain plastids
DNA is located in the nucleus (in eukaryotes),
the mitochondria and
in plastids including chloroplasts
NOTE : The cytoplasm which includes mitochondria
and plastids, are maternally inherited
Sequence it all and No Problem!!!
BUT
1: A huge undertaking
Humans have 23 pairs of chromosomes
or ~65-80,00 genes or ~6,000,000,000 bases
Goldfish have 50-52 pairs of chromosomes
Marsh orchids have 40 or 80 pairs of chromosomes
2: Most is not unique
Humans share 99.4% with chimpanzees,
70% with slugs and 60% with bananas
3: A lot of DNA (not introns) does not apparently code
for anything and much of this is repetitive e.g.
80-90% in humans, 20% in yeast & 15% in
bacteria. “Selfish DNA”.
What Changes Can Be Seen!!
1: Point mutations – single base mutations:
Information on when & where branches in the tree
of life occur.
2: Polyploidy :
Most organisms are diploid (2n).
Sometimes offspring gets 2 sets of paternal and
maternal chromosomes i.e. tetraploid (4n).
(If a new tetraploid breeds with it’s ancestral species (a
backcross), triploid offspring are formed & are sterile.)
In 1928, the Russian plant geneticist Karpechenko produced a new
species by crossing a cabbage with a radish. Although in different
genera (Brassica & Raphanus), both parents have a diploid
number of 18. Fusion of their respective gametes (each n=9)
produced mostly infertile hybrids.
However a few fertile plants were formed, probably by the
spontaneous doubling of the chromosome number in somatic cells
that went on to form gametes (by meiosis). These contained 18
chromosomes - cabbage (n=9) & radish (n=9).
Fusion of these gametes produced vigorous, fully-fertile, polyploid
plants with 36 chromosomes. (Roots of cabbage and leaves of
radish).
These plants could breed with each other but not with the cabbage
or radish, so Karpechenko had produced a new species.
In 1928, the Russian plant geneticist Karpechenko produced a new
species by crossing a cabbage with a radish. Although in different
genera (Brassica & Raphanus), both parents have a diploid
number of 18. Fusion of their respective gametes (each n=9)
produced mostly infertile hybrids.
However a few fertile plants were formed, probably by the
spontaneous doubling of the chromosome number in somatic cells
that went on to form gametes (by meiosis). These contained 18
chromosomes - cabbage (n=9) & radish (n=9).
Fusion of these gametes produced vigorous, fully-fertile, polyploid
plants with 36 chromosomes. (Roots of cabbage and leaves of
radish).
These plants could breed with each other but not with the cabbage
or radish, so Karpechenko had produced a new species.
However
Dactylorhiza (marsh orchids) are split into 2 groups
a: diploid (2n=40)
early marsh,
common spotted,
heath spotted &
frog orchids.
b: tetraploid (4n=80)
irish marsh,
northern marsh,
southern marsh,
hebridean marsh &
Pugsley's marsh
orchid.
Note that they are ALL in
the same genus
What Changes Can Be Seen!!
3: Chromosome rearrangements:
Transposable elements or transposons or “jumping genes”.
Bits of DNA are moved around the chromosomes
directly or via mRNA or incorporation of retroviruses.
Thought to be very important in evolution.
Discovered in a collection of self-pollinated maize plants
by Barbara McClintock for which she was awarded the
1983 Nobel Prize for Physiology and Medicine
What Changes Can Be Seen!!
4: Duplication of genes :
rRNA and dehydrogenases.
5: Spacers between genes:
genetic drift.
The Practical Approach
DNA polyploidy, large transposon insertion and
duplication are useful but such changes are rarely seen
especially with re-classification of closely related species.
Distant relationships best approached by looking at
heavily conserved genes such as those for rRNA, including
mitochondrial rRNA.
Small changes are best observed in selfish DNA or spacers
and most commonly spacers between rRNA genes.
Help is at Hand
Restriction Enzymes or Restriction Endonucleases :
enzymes which cut DNA generally at a 4-6 pair palindromic
sequence on either 1 strand e.g.
~~AGCAGTGACTT~~
or on 2 strands e.g.
~~GGGAATTCAC~~
~~CCCTTAAGTG~~
Sequence is unique for each enzyme (~3000) so get a series of
fragments, the number of & composition of which can be
compared. (Basis of DNA Fingerprinting).
They have been used for phylogeny of nightshade family
(Solenaceae) using chloroplast DNA.
The rRNA Example:
The DNA genes for rRNA are arranged :
18SrRNA - ITS1 - 5.8SrRNA - ITS2 - 28SrRNA - ITS3 - 5SrRNA
& this repeated 1000's of times in tandem.
Advantages of using rRNA spacers (ITS – internal transcibed
spacers)
a: large amounts - less contamination,
b: 'evolutionary drift'.
Used
- together with the intron of chloroplasts to show the legume
family ancestry
- to show the relationships within asteracae, potentilla &
liliaceae
In general, DNA/RNA techniques widely used for fungi and
green algae classification
- and for alcothoe, Brandt’s and whiskered bats
- also with nematodes, yeasts, sponges, bacteria incl. MRSA
and ITS used extensively in the orchids e.g.
frog orchid (right) now considered to be a primitive member
of Dactylorhiza eg early marsh orchid (left)
twayblades (left) now put in Neottia with the birds nest
orchid (right)