Ecosystem • Ecosystem Level: • Ecological Area = number of species (species richness) • Taxonomic definition: Morphology & Life History differences • Molecular genetics Phylogenetics tree construction • Maintain max. diversity of evolutionary lineages • Combining morphological and molecular tools can reveal historical forces = possibly leading to conservation actions or evolutionary explanation of events. • Example: Microbial communities • Ecotones (between forest and savanna) generation of diversity 1
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Ecosystem Ecosystem Level: Ecological Area = number of species (species richness) Taxonomic definition: Morphology & Life History differences Molecular.
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Ecosystem• Ecosystem Level:• Ecological Area = number of species (species richness)• Taxonomic definition: Morphology & Life History differences• Molecular genetics
Phylogenetics tree construction • Maintain max. diversity of evolutionary lineages• Combining morphological and molecular tools can reveal historical
forces = possibly leading to conservation actions or evolutionary explanation of events.
• Example:Microbial communities
• Ecotones (between forest and savanna) generation of diversity
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Defining species
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Taxonomical Point of View
• Groups within a species defined as being of a taxon lower than a species
• Possibly due to population isolation, assortative mating (SSR data)
• Due to a single nucleotide change (Ritland et al (2001) Tyr-to-Cys
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Hybrids
• Interbreeding of two separate species• Using maternal and paternal markers to
determine hybrid zones and extensiveness of the zone
• Conifer species in Abies (paternal cpDNA and maternal mtDNA)
• Using mtDNA, cpDNA and RAPD show hybrid saplings however little adult hybrids
Abies veitchii Abies homolepis
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Hybrids
• Detection of invasive species is very important and an important sign is the detection of hybrids between invasive and native species
• Use of molecular markers are especially important for species that lack many morphological differences
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Individuals• Identification of individuals to species can be difficult
pending on life stage (eg. non flowering plants or tadpoles) or lack of morphological characters
• To delimit a population, it is important to be able to identify individuals
• Biomonitoring by using larvaes is difficult without some kind of unique identifiers
• Barcoding of life project will greatly improve these problems but it will not work for many organisms eg. anaerobic organisms, many plant groups, prokaryotes
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• Forensic investigations calls for identification of suspect and victims
• Use of genetic markers great aid in the investigation
• Recall VNTR marker usage in previous lecture, can use RAPD, AFLP and now a suite of SNP markers to have compare evidential material with known samples (eg. saliva, hair, tree stumps etc.)
Reproduction: determination of Sex• With immaturity and cryptic morphology the
identification of the sex of an individual is not always easy
• To calculate an effective population size the sex of breeding individuals needs to be identify
• Specific primers eg. SRY gene on the Y chromosome can help detect mammalian males
• Appropriate control is required to eliminate “false” females by using a housekeeping gene eg. actin
• Dart samples from whales to identify individuals and the sex of an individuals is an active area of molecular ecology (Barrett-Lennard, Van. Aquarium)
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Determination of Sex
• Exceptions in standard sexing of mammals such as bird (females = WZ, males = ZZ) there is the helicase DNA binding gene (CHD1) which produce different size products for the WZ chromosomes
• Even in plants there is an example of Y (male) specific PCR product eg. hops [diecous plants]
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Prey vs Predator• Predator-prey interactions, most commonly
look at the gut contents to study relationship
• Diet analysis eg. prey “crumbles”• Fecal content eg. coyote diet• Tracking predator eg. gut cells in fecal
matter• Identify individual prey using mtDNA eg.
COI gene, 12S rRNA • Multiple copies of mtDNA great chance of
prey amplification22
Prey vs Predator• Complication of possible secondary prey with PCR
techniques, there is a great chance of this problem with non-invasive sampling
• Some techniques are more problematic eg. RAPD. AFLP
• Usage of specific primers such as SSR will reduce generation of incorrect amplicons, dropout of specific alleles will bias genetic variation estimates
• No techniques are 100% error proof• Replication of 10% of samples will be important
and negative control when doing PCR must be done 23