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Printable Handouts
Navigable Slide Index
- Introduction
- What is conservation biology?
- Sub-discipline: conservation genetics
- Bioinformatics tools give answers to genetics
- Using genetics data: the basic steps
- Working with DNA sequences
- Raw sequence data
- Bioinformatics tools - multiple alignment & editing
- Sequence alignment using GeneDoc
- Sequence alignment using ClustalX
- Sequence alignment using MacClade
- Comparing two different populations
- Measuring population genetic diversity
- Why is genetic diversity important?
- What is genetic diversity?
- Gene diversity
- Gene diversity (H)
- Population A - larger diversity
- Nucleotide diversity
- Number of segregating sites (S)
- The population parameter theta - definition
- The population parameter theta
- Bioinformatics tools - calculating genetic diversity
- Genetic diversity output from DnaSP
- Case studies
- Case study 1: African cheetahs - introduction
- Case study 1: African cheetahs
- Case study 2: humpback whales - introduction
- Case study 2: humpback whales - part 1
- Case study 2: humpback whales - part 2
- More bioinformatics tools: phylogenetic methods
- Identifying populations and ESUs within species
- Tools for identifying distinct evolutionary lineages
- Phylogenetic tree construction methods
- Case studies
- Case study: river dolphin conservation
- Phylogenetic analysis of dolphin mitochondrial DNA
- Case study: Bornean and Sumatran orangutans
- Bornean and Sumatran orangutans - distinct species
- Genetic distance
- Measuring genetic distance - introduction
- Measuring genetic distance
- Measuring genetic distance - phylogenetic tree
- Measuring genetic distance - GeneDoc
- Measuring genetic distance - pairwise distance
- Bioinformatics tools - measuring genetic distance
- Using MEGA to measure genetic distance
- Using MEGA to measure genetic distance - grouping
- Using MEGA to measure genetic distance - results
- Bioinformatics tools application to wildlife forensics
- Two major approaches to wildlife forensics
- Forensics case studies
- Case study: identifying origin of whale products
- Results of whale case study
- Case study: identifying shark products
- How were species-specific PCR primers developed
- Identifying shark species with PCR primers
- PCR amplicons generated by these primers
- Conclusions
Topics Covered
- Conservation biology and genetics
- Working with DNA sequences
- Statistical tools for measuring genetic diversity
- Genetic diversity and conservation: case studies
- Phylogenetic tools for assessing genetic diversity
- Phylogenetics and conservation: case studies
- Measuring genetic distance
- DNA forensics and applications to conservation
Links
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Talk Citation
Shivji, M. and Richards, V. (2017, April 20). Bioinformatics tools in conservation biology [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 26, 2024, from https://doi.org/10.69645/LCQN7707.Export Citation (RIS)
Publication History
Financial Disclosures
- Dr. Mahmood Shivji has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
- Mr. Vincent Richards has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
A selection of talks on Genetics & Epigenetics
Transcript
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0:00
This presentation will review some aspects of the use of
Bioinformatics Tools in the Field of Conservation Biology.
0:09
First, let's define Conservation Biology.
Conservation Biology, which is sometimes also known as Biological Conservation is a field
of scientific study whose practitioners seek to
understand patterns of existing biodiversity,
and how the processes that generate and maintain
biodiversity are influenced by human environmental impacts,
and then use this knowledge to properly manage biological resources to
allow their sustainable use by humans in a way that conserves that biodiversity.
0:45
Now, Conservation Biology as a whole,
is a multidisciplinary field.
One sub-discipline of the field relevant to bioinformatics is conservation genetics,
which is the application of genetic concepts and tools to the study and
conservation of genetic biodiversity in the context of anthropogenic change.
Bioinformatics Tools, many of which are computer programs to analyze
genetic data like DNA and protein sequences have become essential tools for this work.
1:20
Here are some examples of conservation issues that commonly need to be addressed,
and that require the use of bioinformatics.
These include measuring the genetic diversity that exists within populations,
identification and quantification of
genetic differences among populations of the same species.
This is done to determine if the populations represent sufficiently divergent gene pools,
which need to be managed separately as unique evolutionary entities,
which are also known as evolutionarily significant units or ESUs.
Resolving all too common taxonomic uncertainties,
including identification of cryptic species.
After all, you cannot manage and conserve species that you don't know even exists.
Determining if protected and threatened species are being exploited illegally for trade.
A practice that is also disturbingly common
and can lead to species and population extinction.
Let's now look at the basic steps involved in using genetic data in conservation studies.