Conservation Genetics in Raptors

Abstract

Biodiversity is being depleted worldwide at unprecedented rates, due to direct or indirect human actions. These biodiversity losses affect all three fundamental and interrelated levels of biodiversity: ecosystems, species and genetic levels. Conservation genetics emerged in the 1970s as a discipline committed to preserve genetic diversity and minimize the risk of extinction of threatened populations by using genetic tools.

Glossary

Adaptive variation

Changes in the genomes that improve the fitness of individuals to its environments. It is due to natural selection.

Allele

Each of the alternative forms of a gene, locus or nucleotidic sequence

Allelic dropout

Failure of a microsatellite allele to amplify in some of the PCRs reactions. It is a common error when dealing with low quality and quantity of DNA.

Ascertainment bias

Systematic bias in the measure of a frequency associated to how the data has been collected. For instance, ascertainment biases occur when a marker is amplified in a species other than the one it was developed from.

Assay

An investigative procedure used to assess or measure the presence, amount or functionality of an allele.

Codominant

In codominant inheritance, the two alleles in a locus are expressed and make a different variant of the protein.

Electrophoresis

A separating method for proteins or DNA fragments in a gel based on their net charge, size or shape.

Effective population size

The size of an ideal population that experiences genetic drift at the rate of the population in question.

Gene

A part of the genome that can be transcribed to yield a protein.

Genetic diversity

Genetic variation in a population or species. It is a mean of the heterozygous individuals for a locus in a population.

Genetic drift

Evolutionary stochastic process through which allelic frequencies vary from one generation to the next due to random sampling. In small populations genetic drift reduces genetic diversity by eliminating low-frequency alleles and driving others to fixation, ignoring selection.

Gene flow

Transfer of genetic variation from one population to another thanks to migrants.

Genetic erosion

Loss of genetic diversity and increase in inbreeding, especially in small populations.

Genome

Collective term to refer to all the genetic information in an organism. In eukaryotes we consider nuclear, mitochondrial and plastidic as differentiated genomes.

Heterogametic sex

Sex in which the two sexual chromosomes are different.

Inbreeding

Increase in homozygosis due to non-random mating of closely related individuals. Small populations where all individuals are related due to the small size and drift can also have high levels of inbreeding in spite of a random-mating system.

Inbreeding depression

Reduction of fitness (reproduction or survival) due to the increase of homozygosity caused by inbreeding.

Introgression

Incorporation of genes from one population or species to another through hybridization with fertile offspring, which in turn hybridize with parental populations or species.

Kin relationship/kinship

The probability that one allele from one individual is identical by descent to one allele of another individual.

Major Histocompatibility Complex (MHC)

A large family of loci involved in the immune system and the fight to diseases.

Molecular marker

A molecular marker is any trait that can be used as a marker of genetic variation. This variation can exist within or among individuals. A marker is codominant when the expression of heterozygote phenotypes differs from either homozygote genotype. For instance, microsatellites are codominant because they can distinguish a heterozygote (two bands on a gel, two alleles detected by the sequencer, etc.) from a homozygote (single band on a gel).

Monomorphic

A locus in which only one allele is present, in contrast to polymorphic (see below).

Mutation

A change in the DNA sequence.

Null allele

Allele that cannot be detected by PCR due to a mutation in the flanking region that prevents the matching of the oligonucleotide and consequently its amplification.

PCR (polymerase chain reaction)

Consist in making replicate copies (amplify) specific fragments of the DNA sequences.

Panmictic population

A population with random mating.

Primer

A small sequence of nucleotides (18–24 in the case of microsatellite markers), forming a single-stranded chain to which additional nucleotides can be added by a polymerase enzyme. The primer anneals to the DNA of the organism of interest and the enzyme starts copying the template.

Polymorphism

The existence of two or more variants or alleles at a given DNA locus. To be considered a polymorphism, an allele must occur at a minimum frequency of 1%.

Read

Ultimately is the sequence of a section of a unique fragment of DNA produced with next-generation sequencing techniques. NGS produces thousands of millions of reads that are mapped to a reference genome to reconstruct the genome or fragment of the genome of the individual that has been re-sequenced.

Reference genome

Is a database of the sequence of nucleic acids as a representative of the genome of a particular species. It can be assembled from a single or several individuals.

Re-sequencing

It the amplification of the genome of an individual to determine its genomic variations in relation to the reference genome. The sequence generated is aligned to that reference and mined for SNPs, CNVs, genomic rearrangements, etc.