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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)