The weak driver conundrum: data archiving and biological phenomena impact macrogenetic findings

Ivo Colmonero-Costeira, Deborah M Leigh

Macrogenetics seeks to identify the global drivers and patterns in intraspecific genetic diversity, yet many reported patterns are weak or inconsistent. To achieve multispecies global inference, many macrogenetic studies leverage open sequencing data that can suffer from archiving biases. It remains unclear if macrogenetic inconsistencies are innate genetic phenomena, or are the product of open data limitations. Using three widely available genetic markers from the mitochondrion (cytb, co1) and nuclear (TLR4) genomes archived as haplotypes, here we demonstrate archiving biases are powerful enough to distort nucleotide diversity estimates and patterns. Distortion is worsened in analysis using geographic gridded cells, where archiving efforts both outweigh and interact with ecological predictors. Nevertheless, previously described incongruences in drivers of nuclear and mitochondrial diversity appear to be biologically meaningful, indicating some inconsistencies are innate to genetic data.