Marker Selection in Phylogeography

Currently, there is a vast array of molecular markers which can be employed for phylogeographic research. When choosing a molecular marker, it is essential to consider the marker’s mutation rate, inheritance pattern, and the kind of genetic information it provides. Some examples of commonly used (and older) markers are provided below.

Mitochondrial DNA (mtDNA)

Mitochondrial DNA (mtDNA) is a circular, maternally inherited DNA often utilized for studying maternal lineages. One of its primary advantages is the high mutation rate, which provides detailed resolution of genetic differences. The single-parent inheritance simplifies lineage tracing, and its abundance in cells makes it easy to extract and amplify. However, mtDNA only provides information on maternal lineage and its lack of recombination can obscure past hybridization events. Additionally, selective sweeps can reduce genetic variability within mtDNA.

Microsatellites

Microsatellites are short, repetitive DNA sequences dispersed throughout the genome, making them useful for detecting genetic diversity and structure. They exhibit high polymorphism, offering detailed genetic differentiation, and co-dominant markers, allowing the detection of heterozygotes. Microsatellites are effective for fine-scale population studies. Nevertheless, developing species-specific primers for microsatellites is relatively expensive and time-consuming. Their high mutation rates can also lead to homoplasy, where independent mutations result in identical patterns.

Single Nucleotide Polymorphisms (SNPs)

Single nucleotide polymorphisms (SNPs) are single base pair variations within the genome, occurring in both coding and non-coding regions. SNPs can be analyzed in high throughput using genotyping arrays or sequencing, providing genome-wide information. They are suitable for detecting recent genetic differentiation. However, SNPs require prior knowledge of the genome for effective identification and may offer less information per marker due to limited allelic variation.

Restriction Site-Associated DNA Sequencing (RAD-seq)

Restriction Site-Associated DNA Sequencing (RAD-seq) generates genome-wide SNP markers by sequencing regions near restriction enzyme cut sites. RAD-seq offers thousands of markers across the genome and is suitable for non-model organisms. It is effective for understanding fine-scale genetic differentiation. On the downside, RAD-seq requires significant bioinformatics processing, and the sequence coverage can vary between samples, complicating data analysis.

Allozymes

Allozymes are enzyme variants detected by electrophoresis, representing one of the earliest molecular markers used in population genetics. They are co-dominant markers that can detect heterozygosity and are relatively inexpensive and quick to analyze, making them useful for broad-level population studies. However, allozymes have limited resolution compared to modern markers, detect genetic variation only in protein-coding regions, and are less sensitive due to low mutation rates.

Whole-Genome Sequencing

Whole-genome sequencing involves the comprehensive sequencing of an organism’s entire genome, providing the most detailed and exhaustive genetic data available. It can detect rare and previously unknown genetic variants, enabling genome-wide studies of adaptation and population history. Nonetheless, whole-genome sequencing requires advanced sequencing infrastructure, significant computational resources, and extensive data analysis and bioinformatics expertise. The high cost associated with whole-genome sequencing can also limit the sample size.