2.1-classification and biodiversity

• Phylogenetic


  Reflecting evolutionary relatedness.
• Phylogenetic tree


  Diagram showing evolutionary descent, with living organisms at the tips of the branches, ancestral species in the branches and trunk and branch points, representing common ancestors.
• Taxonomy


  The identification and naming of organisms.
• Classification


  Putting items into groups
• Hierarchy


  A system of ranking in which small groups are nested components of larger groups.
• Taxon


  Any group within a system of classification
• Reasons for classification


  A phylogenetic classification system allows us to infer evolutionary relationships

  When describing the health of an ecosystem or the rate of extinction in the geological record, conservationists often find it more useful to count families than species

  Any classification system we use is tentative and may be altered as knowledge advance.
• The three domain system


  A domain is the largest taxon and all living things belong in one of three domains. Domains were originally defined on the basis of rRNA base sequences. More modern methods of analysis also consider similarities in the DNA base sequence.
• The five kingdom system


  This system classifies organisms on the basis of their physical appearance. organisms in different kingdoms have major significant differences.
• Protista

  Some have only one cell major components in plankton. Other cells are colonial. Some are plant-like cells such as spirogyra. Some are animal-like cells such as amoeba. Others have many single cells such as some seaweeds.
• Plantae


  Mosses, horsetails and ferns reproduce with spores. Conifers and flowering plants reproduce with seeds.
• Fungi


  Yeast are single celled. Molds such as Penicillium and mushrooms such as Amanita muscaria have hyphae that weave together to form the body of the fungus.
• Animalia


  The 35 animal phyla include a great range of body plans. Most are motile at some stage of their life.
• Prokaryotae


  Prokaryotes are microscopic. This kingdom contains all the bacteria and cyanobacteria.
• What are the characteristics of Prokaryota


  Organisation- Single-celled

  Nucleus - No

  Mitochondria - Mesosome

  Chloroplast - Some

  Ribosomes - 70s

  ER -No

  Vacuole - No

  Cell Wall - Mesosome

  Nervous Coordination - No
• What are the characteristics of Protoctista


  Organisation - Single and multicellular

  Nucleus - Yes

  Mitochondria - Yes

  Chloroplast - Some

  Ribosomes - 80s

  ER - Yes

  Vacuole - Some

  Cell Wall - Some

  Nervous Coordination - No
• What are the characteristics of Plantae


  Organisation - Multicelular

  Nucleus - Yes

  Mitochondria - Yes

  Chloroplast - Yes

  Ribosomes - 80s

  ER - Yes

  Vacuole - Large and permanent

  Cell Wall - Cellulose

  Nervous Coordination - No
• What are the characteristics of Fungi


  Organisation - Single/hyphal celled

  Nucleus - Yes

  Mitochondria - Yes

  Chloroplast - No

  Ribosomes - 80s

  ER - Yes

  Vacuole - Large and permanent

  Cell Wall - Chitin

  Nervous Coordination - No
• What are the characteristics of Animalia


  Organisation - Multicellular

  Nucleus - Yes

  Mitochondria - Yes

  Chloroplast - No

  Ribosomes - 80s

  ER - Yes

  Vacuole - Small and temporary

  Cell Wall - No

  Nervous Coordination - Yes
• Assessing relatedness with physical features.

  In deciding how closely related two organisms are a biologist looks for homologous structures. They have many different functions, but have a similar form and developmental origin. A good example is the pentadactyl limb of the vertebrates. It is the basic structure in all four classes of terrestrial vertebrates, amphibians, reptiles, birds and mammals. However the limb of the different vertebrates have adapted and have different functions.
• Pentadactyl limb

  
• Homologous structures

  Have a similar arrangement of component parts and a similar developmental origin but different functions.
• Analogous structures

  Have a corresponding function and similar shape, but have a different developmental origin.
• Morphological evidence


  Closely related species are recognized by their similar morphology. Structure similarities are called homologies. They show structures which were present in a common ancestor. The higher the number of homologous structures between two species, the closer they are in the phylogenetic tree.
• Biochemical evidence


  It measures the proportion of genes or proteins between two species to estimate relatedness. These methods can reduce the mistakes made in classification due to convergent evolution.
• Immunological evidence


  The use of blood plasma between species to see their evolutionary relationship. The more precipitate formed the closer the evolutionary relationship.
• Embryological evidence


  Similarities in embryos giving us guidance in the classification. The more similar embryos look the closer they are phylogenetically. This is also evidence that organisms evolved from a common ancestor.
• Behavioural evidence


  Behavioural similarities also provide information about phylogenesis. Humans are classified as primates because:

  Longer period of parental care

  Live in social groups

  Vocalisation and facial expression
• Morphological definition of a species


  If two organisms look very similar they are likely to be in the same species. There may be differences, such as the presence of a mane on male lions but not females. This "sexual dimorphism" must be taken into account when deciding if two organisms are the same species.
• Reproductive definition of a species


  Another way of defining a species states that two organisms are in the same species if they can interbreed to make fertile offspring. Dissimilar organisms may have a different number of chromosomes or incompatible physiology or biochemistry so a hybrid would not be viable.
• Binomial system


  In 1753, Linnaeus introduced a system that gave organisms two names and so was called the binomial system. It has three advantages:

  Unambiguous naming

  Based on Latin, the scholarly language, so could be used all over the world.

  Implies that two species sharing part of their name are closely related.
• Biodiversity as the number and variety of organisms found within a specified geographic region

  The term biodiversity refers to two aspects of organisms in a given environment.

  The number of species, sometimes called species richness.

  The number of organisms, within each species.

  Biodiversity is not constant.
• The number of species and the number of organisms depend, in part, on the environment because

  More plants grow at high light intensity than at low light intensity, so a bright environment can support more herbivores and therefore more carnivores than a dull one.

  More energy flowing through an ecosystem produces more species and more individuals. This means that equatorial regions have a much higher biodiversity than polar regions.
• Biodiversity can increase or decrease for three main reasons

  Succession over time, a community of organisms changes its habitat, making it more suitable for other species. The change in the composition of a community over time is called succession. It increases animal biodiversity but ultimately decrease plant biodiversity.

  Natural selection can generate overtime and change biodiversity.

  Human influence: In many areas of the world, human activity has made the environment less hospitable to living organisms. It has decreased the biodiversity and, in many cases, led to extinction.
• Simpson index calculation

  
• Simpson's index


  Describes the biodiversity of motile organisms.
• Biodiversity can be assessed within a species at a genetic level by looking at the variety of alleles in the gene pool of a population

  An examination of genes and alleles gives an assessment of biodiversity at the genetic level. This approach focuses on all the alleles present in the gene of the population, not on individuals.
• Locus

  Shows polymorphism if it has two or more alleles at frequencies greater than would occur by mutation alone. If a gene has more alleles, its ..... is more polymorphic than if there were fewer.
• Organisms that are more closely related to each other have DNA base sequences that are more ....


  Similar
• These single base differences are called SNPs


  Which stands for Single nucleotide polymorphisms.