07 - Lion Family Reunion: Conservation Biology Genetics
at every nucleotide within a genome, while others are based on much smaller data sets. Moreover, the exact mathematical methods used to analyze the data differ and in some cases, are even kept as tightly guarded company secrets. However, the broad process is consistent and outlined in Figure 1. Scientists begin by collecting DNA samples from many individuals throughout the species’ current range - and sometimes from fossils or museum samples. Using biotechnologies like sequencing or restriction enzyme analysis, they then identify regions of DNA that are variable and that are likely inherited from a single parent (Box 1). These regions are combined, scored, and then categorized as different haplotypes often using letters. Next, each sampled individual is assigned to a haplotype based on his or her genetic profile. This haplotype is then linked back to a location based on where the sample was collected or where the individual was born. Researchers then group samples that are geographically close to each other into populations. Finally, these results are analyzed using a combination of population genetic and phylogenetics. BOX 1: Haplotypes, Just Like Your Mother/Father Haplotypes are unique combinations of DNA polymorphisms that are inherited together and are usually named using letters. While most of an individual’s genome is created by recombination genetic reshuffling activities like meiosis and chromosomal crossover that create a unique genetic mixture of both parent’s DNA - there are DNA regions that are inherited together from a single par- ent. DNA that meets this criterion includes that found in mitochondria plasmids, plant chloroplasts plasmids, and (in humans) the Y chromosome. In some cases, genomic DNA – genetic material that occurs in paired chromosomes and undergoes recombination - can still be used like a haplotype provided that it is subdivided into subunits of very closely spaced or “linked” regions. Because they are inherited relatively unchanged from parent to child haplotypes are much easier to trace back in time! In many cases, phylogeographers will construct several histories based on different haplo - type-types (i.e. a mtDNA haplotype and a Y chromosome haplotype) as each tells a slightly different history that both complements and double-checks the other histories. Population genetics is a subfield of genetics that deals with genetic differences within and between populations. In phylogeography, scientists pay particular attention to which haplotypes are unique to a single population and which are shared by many populations as well as the number of haplotypes observed in each population. This information is described using mathematically based measures like effective population size, expected heterozygosity and F-statics. It is also visually summarized by pie graphs of each population’s haplotypes added to a map of each population’s location (Figure 2). To- gether, population genetic statistics and haplotype maps describe the genetic patterns of a species or the “geography” part of its phylogeography.
Figure 2: An example genetic map - human mtDNA haplotypes.
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