Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

Abstract

Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to resolve phylogenetic trees, but the diploid nature of sequence data remains analytically challenging. Here, we performed a phylogenomic reconstruction of the evolutionary history of the common vole (Microtus arvalis) with a focus on the influence of heterozygosity on the estimation of intraspecific divergence times. We used genome-wide sequence information from 15 voles distributed across the European range. We provide a novel approach to integrate heterozygous information in existing phylogenetic programs by repeated random haplotype sampling from sequences with multiple unphased heterozygous sites. We evaluated the impact of the use of full, partial, or no heterozygous information for tree reconstructions on divergence time estimates. All results consistently showed four deep and strongly supported evolutionary lineages in the vole data. These lineages undergoing divergence processes split only at the end or after the last glacial maximum based on calibration with radiocarbon-dated paleontological material. However, the incorporation of information from heterozygous sites had a significant impact on absolute and relative branch length estimations. Ignoring heterozygous information led to an overestimation of divergence times between the evolutionary lineages of M. arvalis. We conclude that the exclusion of heterozygous sites from evolutionary analyses may cause biased and misleading divergence time estimates in closely related taxa.

Continental-Scale Footprint of Balancing and Positive Selection in a Small Rodent (Microtus arvalis)

“…Similar patterns were found in humans were genetic data also mirror geography in Europe [84]. This high resolution indicates the large information content present in this AFLP data set and is further supported by a very similar PCA-based clustering of populations inferred by 6,807 polymorphic SNPs (see Figure S2 in [60]), which were used to resolved the four evolutionary lineages present in Europe [43].…”

“…[91], [95], [96]). An alternative strategy would be the investigation of candidate loci for selection by direct high-throughput sequencing of AFLP fragments [60], [97], which could be useful to further characterize candidate regions and genes linked with AFLP markers in this non-model organism.…”

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

“…Indeed, simulation studies have shown that the concatenation procedure can provide high statistical support for an incorrect species tree, because lineage sorting processes are not modeled (Kubatko and Degnan 2007). Finally, branch length estimates are affected when heterozygous sites are excluded from phylogenetic analyses (Lischer et al 2014), which was common practice in phylogenetic analyses of concatenated autosomal data. Conceptual advances and recently developed coalescence-based multilocus species tree approaches now provide a means to infer overall phylogenetic relationships (species trees), against which individual gene trees can be contrasted to identify the underlying evolutionary processes.…”

Triplicate parallel life cycle divergence despite gene flow in periodical cicadas

“…Therefore, we employed the repeated random haplotype sampling (RRHS) strategy 62 when phase information was required. RRHS randomly assigns one of two possible genotypes at heterozygous sites.…”