A common method of minimizing errors in large DNA sequence data sets is to drop variable sites with a minor allele frequency (MAF) below some specified threshold. Although widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical single nucleotide polymorphism data set to demonstrate the impacts of MAF thresholds on inference of population structure—often the first step in analysis of population genomic data. We find that model‐based inference of population structure is confounded when singletons are included in the alignment, and that both model‐based and multivariate analyses infer less distinct clusters when more stringent MAF cutoffs are applied. We propose that this behaviour is caused by the combination of a drop in the total size of the data matrix and by correlations between allele frequencies and mutational age. We recommend a set of best practices for applying MAF filters in studies seeking to describe population structure with genomic data.

Aim In response to warming, species are shifting their ranges towards higher elevations. These elevational range shifts have been documented in a variety of taxonomic groups across latitude. However, the rate and direction of species range shifts in response to warming vary, potentially as a consequence of variation in species traits across elevation. Specifically, diurnal and seasonal climates are often more variable at higher elevations, which results in high‐elevation species that have broader thermal physiologies relative to low‐elevation species. High‐elevation species that are thermal generalists might not need to move as far to track their thermal niche as low‐elevation thermal specialists. We investigated whether rates of range shifts varied systematically with increasing elevation across taxa and regions. Location Sixteen montane regions world‐wide. Time period 1850–2013. Taxon Nine hundred and eighty‐seven species of plants and animals. Methods We gathered published data on elevational range shifts from 20 transect studies comparing historical and recent distributions and examined how rates of range shifts changed across elevation. Specifically, we performed a meta‐analysis to calculate the pooled effect of elevation on species range shifts. Results We found that rates of range shifts show a negative relationship with elevation such that low‐elevation species have moved upslope farther than high‐elevation species on the same transect. This finding was primarily a result of shifts in the upper range limits. We also found that 28% of species shifted downslope against predictions, but elevation did not show a relationship with downslope range shifts. Main conclusions Idiosyncratic range shifts will significantly alter montane ecological communities, which are home to some of the greatest biodiversity on Earth. Our results demonstrate that species range shifts vary with elevation and might be a consequence of differences in species traits that also vary along montane gradients.

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

Laboratory techniques for high‐throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site‐associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site‐associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.