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.
Abstract.-Across the genome, the e↵ects of di↵erent evolutionary processes and historical events can result in di↵erent classes of genetic variants (or alleles) characterized by their relative frequency in a given population. As a result, population genetic inference can be strongly a↵ected by biases in laboratory and bioinformatics treatments that a↵ect the site frequence spectrum, or SFS. Yet despite the widespread use of reduced-representation genomic datasets with nonmodel organisms, the potential consequences of these biases for downstream analyses remain poorly examined. Here, we assess the influence of minor allele frequency (MAF) thresholds implemented during variant detection on inference of population structure. We use simulated and empirical datasets to evaluate the e↵ect of . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/188623 doi: bioRxiv preprint first posted online Sep. 14, 2017; MAF thresholds on the ability to discriminate among populations and quantify admixture with both model-based and non-model-based clustering methods. We find model-based inference of population structure is highly sensitive to choice of MAF, and may be confounded by either including singletons or excluding all rare alleles. In contrast, non-model-based clustering is largely robust to MAF choice. Our results suggest that model-based inference of population structure can fail due to either natural demographic processes or assembly artifacts, with broad consequences for phylogeographic and population genetic studies. We propose a simple hypothesis to explain this behavior and recommend a set of best practices for researchers seeking to describe population structure using reduced-representation libraries.(Keywords: MAF; population structure; population genetic inference; structure; clustering; genomics; bioinformatics)The distribution of genetic variation within and among individuals is the crucial to understanding the organization of biological diversity and its underlying causes. Across the genome, the e↵ects of di↵erent evolutionary processes and historical events can result in di↵erent classes of genetic variants (or alleles) characterized by their relative frequency in a given population. An excess of common alleles may reflect the signature of population bottlenecks (Marth et al. 2004), purifying selection (Fay et al. 2001), or the absence of population subdivision (Pritchard et al. 2000). Alternatively, high frequencies of rare alleles can provide evidence of population expansion (Marth et al. 2004), detailed information on mutation rates and gene flow (Slatkin 1985), and reveal geographically localized population subdivision (Barton and Slatkin 1986;Gompert et al. 2014). Because the distribution of allele frequencies (also known as the site frequency spectrum, or SFS). CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The co...
Tropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.
Rapid species turnover in tropical mountains has fascinated biologists for centuries. A popular explanation for this heightened beta diversity is that climatic stability at low latitudes promotes the evolution of narrow thermal tolerance ranges, leading to local adaptation, evolutionary divergence and parapatric speciation along elevational gradients. However, an emerging consensus from research spanning phylogenetics, biogeography and behavioural ecology is that this process rarely, if ever, occurs. Instead, closely related species typically occupy a similar elevational niche, while species with divergent elevational niches tend to be more distantly related. These results suggest populations have responded to past environmental change not by adapting and diverging in place, but instead by shifting their distributions to tightly track climate over time. We argue that tropical species are likely to respond similarly to ongoing and future climate warming, an inference supported by evidence from recent range shifts. In the absence of widespread in situ adaptation to new climate regimes by tropical taxa, conservation planning should prioritize protecting large swaths of habitat to facilitate movement.
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