Species, Classification and Biodiversity

• Classification:

  • there is a vast range of different organisms present on this planet. About 1.8 million different species on earth have so far been identified and named and there are likely many more yet to be discovered (possibly up to 9 million)
  • scientists need to sort out and classify these organisms using patterns of similarities and differences
  • classification - the way in which living organisms are divided into groups
  • taxonomy - the scientific practice of grouping organisms based on shared characteristics. Each group is called a taxon (plural - taxa)
• Modern classification systems:

  • most modern-day classification systems do not just group organisms based on easily observable features but use many different sources of evidence (fossil records, cell ultrastructure, biochemistry, molecular biology, behaviour)

  they are also;

  • hierarchal - consist of large groups that are divided into progressively smaller groups with no overlap between the groups
  • phylogenetic - based on the evolutionary history of organisms (i.e. their common ancestry)
• Taxonomic ranks:

  the most used classification system includes eight taxonomic ranks;

  • domain
  • kingdom
  • phylum (plural - phyla)
  • class
  • order
  • family
  • genus (plural - genera)
  • species

  they are listed in descending order of size, so that domain is the largest group (in total there are three domains - eukaryote, bacteria and archaea) and species contain the fewest organisms. Non-overlapping means each organism can only appear in one group at a particular taxonomic level
• Classification:

  • all living organisms are currently classified into six kingdoms; bacteria, archaea, protoctista, fungi, plants and animals
  • all mammals are classified in the same kingdom, phylum and class. At the next level - order - the mammals begin to diverge until only those organisms with the greatest similarities share the species level
  • two organisms belong to the same species if they are similar and can breed with each other to produce fertile offspring
  • the further down the groups you go, the more closely related the species are that are in that group
• Binomial naming system:

  • the biological name of a species is derived from its genus and species names (a binomial naming system)
  • the first is the genus name and always has a capital letter
  • the second is the species name and always has a small letter
  • the full name is printed in italics or underlined if handwritten
  • using this system means there is no confusion as to exactly what species is being referred to. It allows research to be shared between countries with different languages, ensuring nothing is mistranslated
• Phylogenetic system:

  • this reflects the evolutionary relationship between organisms. It looks at similarities and differences in structure and function
  • the relationships are usually represented by a diagram called a phylogenetic tree, with the oldest species at the base of the tree and the most recent ones are represented by the end of the tree
  • each branch represents where divergence occurs (i.e where a common ancestor evolves to become new species). The closer the branches, the closer the evolutionary relationship, therefore the more recently they shared a common ancestor
• Courtship behaviour:

  • courtship behaviour is innate; it is genetically determined
  • all members of the same species are genetically programmed to show the same courtship behaviour as they have the same genes
  • members of different species show different behaviours
  • therefore, the courtship behaviour can be used to identify individuals as members of the same or different species
• Clarifying evolutionary relationships:

  • classifying organisms according to their evolutionary relationships is not easy, particularly if based just on using observable characteristics
  • however, advances in DNA and molecular technology are helping us classify organisms more accurately
  • this can lead to classification systems being updated

  Technologies that have been useful for clarifying evolutionary relationships include;

  • genome sequencing
  • comparing amino acid sequences
  • immunological comparisons
• Problems in classifying organisms as distinct species:

  systems and ideas constantly change as new evidence and techniques come to light;

  • life probably evolved around 3.5 billion years ago and the extinct species greatly outnumber the living ones
  • most species did not leave fossils and even when fossils have been found, they are often incomplete and not all features can be observed
  • if the organisms are only known from fossil records, we cannot test whether they can interbreed and produce fertile offspring
  • there is considerable variation within any one species
  • groups of organisms that are isolated from each other (e.g. by oceans)may be classified as different species. However, they may turn out to be the same species if their ability to interbreed is tested (often difficult to test in practice)
  • the ability to interbreed cannot be tested on organisms that use asexual reproduction
• Investigating genetic diversity:

  there are several ways that genetic diversity within or between species can be measured;

  • investigating genetic diversity by comparing the frequency of measurable or observable characteristics
  • investigating genetic diversity by comparing the base sequence of DNA
  • investigating genetic diversity by comparing the base sequence of mRNA
  • investigating genetic diversity by comparing the amino acid sequence of the proteins encoded by DNA and mRNA
  • investigating genetic diversity using immunological techniques
• Investigating genetic diversity by comparing the frequency of measurable or observable characteristics:

  • before modern gene technology, genetic diversity could only be investigated through careful detailed observations of the anatomy and physiology of different individuals
  • however, observable characteristics are often coded for by more than one gene (polygenic). The environment can also influence some characteristics so does not directly shows differences in an organism's DNA e.g. skin colour, weight, height
  • phenotype is usually the result of interaction between genetic factors and environmental factors
• Investigating genetic diversity by comparing the frequency of measurable or observable characteristics:

  characteristics controlled by one or two genes show discontinuous variation;

  • variables are assigned to clearly defined categories or distinct groups
  • examples include; sex, blood groups, eye colour
  • data is usually presented as a bar graph
  • the variables are discrete

  polygenic characteristics (characteristics coded for by more than one gene) and those influenced by environmental factors show continuous variation;

  • gives a full range of variables between 2 extreme values
• Investigating genetic diversity by comparing the base sequence of DNA:

  • members of the same species will have very similar base sequences of DNA
  • over time, as populations evolve, random mutations will accumulate and cause genetic variation
  • species that have closer evolutionary relationships and share a more recent common ancestor will have more similar bases sequences of DNA in a particular gene than species that have diverged on different evolutionary paths a longer time ago
  • modern gene technology has made it possible to compare DNA directly
• Investigating genetic diversity by comparing the base sequence of mRNA:

  • sometimes it is more useful to compare organisms by looking at which parts of their genomes are expressed and directly form proteins (mRNA has no introns)
  • looking at how the base sequence of mRNA varies can be used to investigate diversity both between and within species
• Investigating genetic diversity by comparing the amino acid sequence of the proteins encoded by DNA and mRNA:

  • as DNA base sequences codes for the sequence of amino acids in proteins, organisms that share a recent common ancestor and are more closely related will have similar amino acid sequences when looking at a particular protein
• Investigating genetic diversity using immunological techniques:

  • to investigate other organism's evolutionary relationship to humans, blood serum from different organisms can be mixed with antibodies complementary to human blood proteins
  • organisms with blood containing similar proteins to humans will result in a greater amount of 'precipitation' when mixed with human antibodies, suggesting they share a more recent common ancestor
• Biodiversity:

  • biodiversity is a general term used to describe the variety of living organisms in a community/habitat

  key terms when discussing biodiversity;

  • population - all the organisms of the same group or species that live in an area
  • habitat - the place where an organism lives
  • community - all the organisms (of different species) in a habitat
  • interspecific - the variation that exists between different species
  • intraspecific - the variation that occurs within a species
  • genetic diversity - the variety of genes possessed by individuals that make up any one species
  • ecosystem diversity - the range of different habitats within a particular area
• Species richness and diversity:

  • species richness - this is the number of different species in a habitat (but this does not take into account the number of different individuals in that species)
  • species diversity - the number of different species and the number of individuals of each species within any one community. This can be calculated using the Species Diversity Index
• Species diversity index:

  to compare two samples, we need to calculate the Species Diversity Index, a single number which we can use to describe species diversity. The diversity of a community reflects;

  • the number of different species present
  • the number of individuals in each species

  high biodiversity has a higher number of different species and a higher number of individuals within each species
• Species diversity index:

  • the index of diversity enables us to make and objective assessment f diversity in any community
  • the diversity index is calculated using the following formula;

  d = (N(N-1) ÷÷ ($\sum_{ }^{ }$n (n-1))

  • d = diversity index
  • N = total number of organisms of all species
  • n = total number of organisms of a particular species
  • $\sum_{ }^{ }$= sum of
• Using the diversity index:

  • low value -the nature of the environment is unfavourable/harsh (desert, Arctic tundra, upper seashore) . Few species present and often populations are small. Generally, abiotic (non-living) factors determine which species are present. Ecosystems in these environments are usually unstable. Only a few species are adapted to survive in the harsh conditions
• Using the diversity index:

  high value - the nature of the environment is favourable (tropical rainforest, temperature woodland, lower seashore). Many species present and populations are usually large. If there is a high diversity of plants and trees, there will be a high diversity of insects, animals and birds as there are more habitats, food source etc. This is because if there are more plants and trees, herbivores will colonise the area, and then carnivores will follow. Generally, biotic (living) factors, such as competition and predation, determine which species are present. Ecosystems in these environments are usually stable. Complex food webs so a change in population of one species is less likely to affect other populations
• Impact of agriculture:

  • modern intensive farming usually involves the removal of existing vegetation and the growth of one crop species, a system called monoculture
  • the aim is to provide ideal conditions for the crop to grow and supply a high yield
• Ideal agricultural conditions:

  agriculture provides ideal conditions for crop photosynthesis and growth by;

  • fertilisers added to provide minerals for growth
  • field irrigated so there is enough water
  • the crop species themselves are specially selected to grow well in the conditions provided (e.g. to make use of the fertiliser and grow fast to outcompete weeds), and to provide high yields of useful product
  • weeds are prevented from growing on the land as they compete with the crops for resources
  • animals which compete with us by eating the crop such as insect pests are also removed
• Ideal agricultural conditions:

  • weeds can be physically picked out as they start to grow, or chemical herbicides can be used which kill the weeds but not the crop plants
  • animal pesticides (e.g. insecticides) are toxic chemicals which usually kill a wide range of similar species
  • in addition to this, removing hedgerows and field boundaries, unprofitable pockets of woodland and draining marshy areas make maximum use of land for crops, and remove sources of pests and disease
  • the effect of this is to produce fields where only one plant species grows, perhaps with a few weeds and animals which feed on the crop
• Monoculture (growing just 1 crop/plant type):

  • a low variety of habitats/niches
  • few plant species because just one crop species is grown and most weed are removed or killed by herbicides
  • few species of herbivores as so little variety of plant food types
  • fewer types of carnivore species because so few herbivore species to feed on
  • use of pesticides will reduce diversity of insect species
• High species diversity (i.e. an area with lots of different species and lots of different individuals of each species):

  • a high variety of habitats/niches
  • many plant species because many plants grow here
  • many species of herbivores as so many different varieties of plant food types
  • more types of carnivore species because so many herbivore species to feed on
• Conservation methods:

  • maintain existing hedgerows at the most beneficial height and shape. An A-shape provides better habitats than a rectangular one
  • plant hedges rather than erect fences as field boundaries
  • maintain ponds and where possible creates new one
  • leave wet corner of fields rather than drain them
  • plant native tree species on land with low species diversity rather than in species-rich disease areas
  • reduce the use of pesticides - use biological control where possible or genetically modified organisms that are resistant to pests
• Conservation methods:

  • use organic, rather than inorganic, fertilisers
  • use crop rotations that includes a nitrogen-fixing crop, rather than fertilisers, to improve soil fertility
  • create natural meadows and use hay rather than grasses for silage
  • leave the cutting of verges and field edges until after flowering and when seeds have dispersed
  • introduce conservation headlands - areas at the edge of fields where pesticides are used restrictively so that wildflowers and insects can breed
• Sampling:

  • in practice measuring the Species Diversity Index involves sampling
  • it is impossible to identify and count all the individual organisms in an area as this would be too time consuming and is likely to cause a lot of damage to the community
• Sampling:

  the sample needs to be;

  • large - large samples are more representative of the population than small samples and minimise the influence of chance on the results. However, the size of the sample is often determined by the time available to collect the sample. A mean is calculated from the large sample
  • taken via random sampling to ensure that every member of the population has an equal chance of being included in the sample. This avoids sampling bias
• Method for sampling:

  to study variation, a sample needs to be taken;

  • a grid is laid out across the sample area using tape measures
  • random numbers are generated (from a calculator or a random number generator/table) to provide coordinates on the grid. These are the sample points where a quadrat is placed
  • within each quadrat the community is identified and either counted individually (species density), the % cover is calculated, or the frequency of the species is counted, using the north-east rule
  • as any one sample point is unlikely to be representative of the area, a large number of randomly placed quadrats are used
• Sampling:

  once the sample has been taken, a mathematical test should be done;

  • index of diversity (D)
  • standard deviation to ensure any differences in results are not due to chance
  • a statistical test
• Standard deviation:

  • this is the measure of the spread of values about the mean and therefore indicates the extent of variation a population shows

  the smaller the standard deviation;

  • more similar the data is an so there is less variation
  • the more reliable the data is
• Standard deviation:

  • using standard deviation is more valid than using the range as the standard deviation reduces the impact of extreme data points (anomalies), unlike the range, which is just the difference between the highest and lowest values
  • SD is written as mean +/- SD
  • standard deviation can be shown in a data table or on a graph in the form of bars, drawn above and below the mean

  standard deviation is useful for comparing two or more sets of data. The standard deviation can be calculated for each set of data;

  • if the standard deviations overlap, then there is no significant difference
  • if the standard deviations do not overlap, then there is a significant difference