Mitochondrial DNA is unsuitable to test for isolation by distance

Abstract

Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species’ true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.

The Out of East Asia model versus the African Eve model of modern human origins in light of ancient mtDNA findings

“…Indeed, the 45000 year old Ust’-Ishim’s mtDNA had fewer SNPs to begin with and the one he did have are all common alleles in today’s population (>67%) except one site 16150 10 . The Asia model also regards mutations in mtDNA to be functional, which has ample evidential support 26,33,42,43 , and classifies haplotypes based on sharing of alleles with more weight on the slow evolving sites (altering protein or RNA sequences) 5 . Hence, the Asia model is inherently more sound and self-consistent than the Africa model due to stronger theoretical foundations and far more realistic assumptions.…”

Whole genome single nucleotide polymorphism genotyping of <i>Staphylococcus aureus</i>

“…The regions with rich SNPs may have high mutation rates and are more likely to undergo recurrent mutations. Therefore, it is expected that high SNP regions may not follow the infinite site assumption and may cause uncertainness for building phylogenetic trees (Teske et al, 2018;Kern and Hahn, 2018). Despite some similar topologies in high SNP and SNP trees, the rare SNP may provide more meaningful evolutionary history of bacteria.…”

“…In evolution analysis, high SNP regions usually do not follow the infinite site assumption and may cause uncertainty for building phylogenetic trees (Teske et al, 2018;Kern and Hahn, 2018). Genomic regions with rich SNPs have high mutation rates and are more likely to undergo recurrent mutations.…”

Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential

“…Alleles in Space (Miller, 2005) was used to correlate matrices of pairwise genetic distances (Φst) between all populations with geographic distances using a Mantel matrix correspondence test and produce scatterplots. Despite the limitations of this test in mtDNA analyses, usually lumping populations without pointing to Isolation by Distance in non-structured populations (Teske et al, 2018), we used the Mantel test to explore the data, interpreting the results according to Hutchinson & Templeton (1999).…”