Genetic markers for Biodiversity analyses
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Resumo do trabalho
Trabalho do curso de Biologia dedicado ao tema "Genetic markers for Biodiversity analyses" (em inglês)...
Genetic markers for Biodiversity analyses
Genetic markers are heritable characters with multiple states of each character, and reflect differences in DNA sequences. Methods to determine genetic variation on the DNA level include fingerprint methods, length polymorphisms and sequencing.
Minisatellites are tandem repeat sequences that show length polymorphism arising from unequal crossing-over or gene conversion. Hybridization of genomic DNA with a minisatellite core sequence produces a bar-code line hybridization pattern.
This technique is not very used in population genetics and genome mapping. It presents complex banding pattern that difficult the assignment of alleles to a given locus. Population genetic analyses cannot be applied to minisatellite data also because of its non-random distribution in the genome. Later, single locus minisatellites were developed, but most markers required a high-molecular DNA and its development it’s not a very easy procedure.
Microsatellites are also tandem repeated sequences, but the tandem motifs are shorter than minisatellites. With repeat regions smaller than 100 bp, most microsatellites can be amplified by PCR. They are abundant, highly polymorphic, informative and evenly distributed in the euchromatic part of genomes. Microsatellites are generally used markers for population genetics and its high mutation rate offers a more detailed analysis of their mutation pattern.
The high mutation rate of microsatellites can be used to infer past demographic events.
These markers can be also analysed as individual genes with frequencies and geographic distribution, and this data can be used in studies about gene flow and population history, even in species with low genetic diversity. Microsatellites are also suitable to detect highly divergent cryptic species, interspecific gene flow and high level of genetic recombination.
But the mutation pattern can be to complex and can be difficult to apply it to population genetic analyses. Also the density of informative microsatellites loci can be very low.
RAPDs, AFLPs, RFLPs
Another class of PCR based markers.
These techniques do not require a priori knowledge about primer sequences in the target species. PCR amplification yields multiple bands that show the variation among individuals.
The inheritance is dominant, so fragments can only be scored as present or absent. But a substantial proportion of the variability these methods detect can be nonheritable. Allele frequencies are rarely available.
These techniques produce multilocus data that can be difficult to compare between studies because the inferences obtained from pattern analyses only have meaning for a concrete study. The data obtained can also be unreliable, so diversity studies based on these techniques are discouraged.
The use of sequence polymorphism as markers has been common since the first RFLP studies. SNPs are suitable for automated highthroughput analysis at an acceptable cost.
SNPs are single nucleotide position, but within a population most nucleotide positions are invariant and a priori information of the mutation at a given position is required.
SNPs are useful for past demographic events and detection of population expansion or admixture. As SNPs are usually biallelic, the information obtained from a single SNP is limited, especially if one of the alleles occurs at a low frequency. Ascertainment bias can occur producing false results, so SNP-based approaches depend on a appropriate correction of this bias. Despite this markers development is time and cost intensive, several methods for estimating population parameters could be applied to SNPs.
Gene sequencing of a given region in multiple individuals provides accurate genetic information. This method has been widely used in population genetics to infer selection and demographic patterns. Recent advances in sequencing technology permit sequence analysis of many DNA fragments for many individuals. There is no ascertainment bias and we can get complete information from the analysed region. Invariable sites are also sequenced, and especially for species with low polymorphism, sequencing might be uneconomic. But the invariant sites can be informative if appropriate analysis tools are used.
DNA sequencing of multiple genomic regions is a safe approach to estimate demographic history, and demographic analyses and neutrality tests are well-developed for the use of sequencing data.